Difference: CemSiteMap (1 vs. 30)

Revision 3002 Jan 2013 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"

Overview

Interested in Cryoem? (How to begin a project) CemInterested
Cryoem at NYSBC CemIntroduction
General info on cryoem at NYSBC CemGeneralInfo
Cryoem Operations committee CemOpCom
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
Overview of negatively-staining proteins for EM CemNegativeStain
How to sign up for CEM equipment at NYSBC CemSignupOverview
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
Publications related to CEM at NYSBC CemPublications
CEM Newsletter NewsLetter
Added:
>
>
Ed's Cartoon overview of EM CemCartoonOverview
 
The site map you are now viewing CemSiteMap

Equipment

Equipment overview - Sample preparation CemSamplePrep

Plasma cleaners

Plasma cleaners CemPlasmaCleaning
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
Glow Discharge Using Edwards Evaporator GlowDischarge

Cryo

Plunge freezing equipment CemPlungeFreezer
High Pressure Freezing Menu HighPressFreezer
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
Use of the Oscilloscope/ Matlab MatlabOscilloscope
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Main page for all Microscopes CryoEM
Microscope overview page CemMicroscopes
CEM Parameters CemParameters
How to Find The Beam FindBeam
Microscope Shut Down ShutDown

Jeol 1230

Jeol 1230 description Jeol1230Description
Jeol 1230 Information Jeol1230Information
Jeol 1230 Instructions Jeol1230Instructions
Jeo l1230 filament exchange instructions FilamentExchange

Jeol 2100

Jeol 2100 description Jeol2100Description
Jeol 2100 Information Jeol2100Information
Jeol 2100 Basic Instructions Jeol2100Basicinstructions
Jeol 2100 Instructions Jeol2100Instructions

Jeol 3200

Jeol 3200 description Jeol3200Description
Jeol 3200 Information Jeol3200Information
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
Tecnai Information TecnaiInformation
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
Tecnai Instructions TecnaiInstructions
Tecnai advanced instructions TecnaiAdvanced
Ccd Blank Enable, specific for Tecnai F20 CcdBlankEnable
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

FEI Helios Dual Beam overview HeliosDescription
Helios Instructions CemHeliosInstructions

Light Microscope

Nikon Eclipse Ti-U CemNikonEclipse
Basic Instructions for Nikon Ti-U NikonTiInstructions
How to deal with uneven grid? NikonTiFocusSurface
Overview of CLEM workflow CemCLEM

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage

Automated Data Collection

Automated data collection with Serial EM SerialEM
Older notes on Serial EM SerialEmNotes
Serial EM Macros SerialEMMacros
Notes on Shutter Box settings on Tecnai on Low Dose and Serial EM ShutterBox
Serial EM - notes on montages and use of the Navigator MontageNavigator
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList

Film Related

Film Screening And Scanning Overview FilmScreeningAndScanning
Scanning - PDS Densitometer PdsDensitometer
Scanning - Zeiss Densitometer ZeissDensitometer
Screening films with Optical Bench OpticalBench

Lab Protocols

Main protocols page CemProtoc

Grid Preparation

Grid prep - general information CemProtocGrids
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
Plastic Coated Grid PlasticCoatedGrid
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Considerations for electron tomography sample preperation CemProtocET
Fiducial Markers for Tomography PPFiducialsTomography
Carbon Coating instructions CarbonCoating
Carbon Coating using Thread CarbonThread
Carbon Coating using Carbon Rod CarbonRod
Metal Shadowing MetalShadowing
Rotary Shadowing CemRotaryShadowing

Staining

Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining

Cryo

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
High pressure freezing CemProtocHPFU
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc

Image Processing

Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
EmIP - How to Plot 1D CTF profile of an image FileConversion
Helical Processing : Initial steps HelicalProcessing
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
Helical Reconstruction with EmIP HelicalReconstruction
Processing - electron crystallography CemProtocProcessEC
Processing - tomographic data CemProtocProcessET
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Processing - Single particle analysis CemProtocProcessSPA
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

CEM Facility

CEM Newletter Archive NewsLetter
Facility Announcements CEMAnnouncements

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub


General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. All mirrored sites can be found on: CemTwikiToWebList. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact the CEM staff.

  • Set ALLOWTOPICVIEW =

Revision 2920 Dec 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"

Overview

Interested in Cryoem? (How to begin a project) CemInterested
Cryoem at NYSBC CemIntroduction
General info on cryoem at NYSBC CemGeneralInfo
Cryoem Operations committee CemOpCom
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
Overview of negatively-staining proteins for EM CemNegativeStain
How to sign up for CEM equipment at NYSBC CemSignupOverview
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
Publications related to CEM at NYSBC CemPublications
CEM Newsletter NewsLetter
The site map you are now viewing CemSiteMap

Equipment

Equipment overview - Sample preparation CemSamplePrep

Plasma cleaners

Plasma cleaners CemPlasmaCleaning
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
Glow Discharge Using Edwards Evaporator GlowDischarge

Cryo

Plunge freezing equipment CemPlungeFreezer
High Pressure Freezing Menu HighPressFreezer
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
Use of the Oscilloscope/ Matlab MatlabOscilloscope
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Main page for all Microscopes CryoEM
Microscope overview page CemMicroscopes
CEM Parameters CemParameters
How to Find The Beam FindBeam
Microscope Shut Down ShutDown

Jeol 1230

Jeol 1230 description Jeol1230Description
Jeol 1230 Information Jeol1230Information
Jeol 1230 Instructions Jeol1230Instructions
Jeo l1230 filament exchange instructions FilamentExchange

Jeol 2100

Jeol 2100 description Jeol2100Description
Jeol 2100 Information Jeol2100Information
Jeol 2100 Basic Instructions Jeol2100Basicinstructions
Jeol 2100 Instructions Jeol2100Instructions

Jeol 3200

Jeol 3200 description Jeol3200Description
Jeol 3200 Information Jeol3200Information
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
Tecnai Information TecnaiInformation
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
Tecnai Instructions TecnaiInstructions
Tecnai advanced instructions TecnaiAdvanced
Ccd Blank Enable, specific for Tecnai F20 CcdBlankEnable
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

FEI Helios Dual Beam overview HeliosDescription
Helios Instructions CemHeliosInstructions

Light Microscope

Nikon Eclipse Ti-U CemNikonEclipse
Basic Instructions for Nikon Ti-U NikonTiInstructions
How to deal with uneven grid? NikonTiFocusSurface
Added:
>
>
Overview of CLEM workflow CemCLEM
 

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage

Automated Data Collection

Automated data collection with Serial EM SerialEM
Older notes on Serial EM SerialEmNotes
Serial EM Macros SerialEMMacros
Notes on Shutter Box settings on Tecnai on Low Dose and Serial EM ShutterBox
Serial EM - notes on montages and use of the Navigator MontageNavigator
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList

Film Related

Film Screening And Scanning Overview FilmScreeningAndScanning
Scanning - PDS Densitometer PdsDensitometer
Scanning - Zeiss Densitometer ZeissDensitometer
Screening films with Optical Bench OpticalBench

Lab Protocols

Main protocols page CemProtoc

Grid Preparation

Grid prep - general information CemProtocGrids
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
Plastic Coated Grid PlasticCoatedGrid
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Considerations for electron tomography sample preperation CemProtocET
Fiducial Markers for Tomography PPFiducialsTomography
Carbon Coating instructions CarbonCoating
Carbon Coating using Thread CarbonThread
Carbon Coating using Carbon Rod CarbonRod
Metal Shadowing MetalShadowing
Rotary Shadowing CemRotaryShadowing

Staining

Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining

Cryo

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
High pressure freezing CemProtocHPFU
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc

Image Processing

Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
EmIP - How to Plot 1D CTF profile of an image FileConversion
Helical Processing : Initial steps HelicalProcessing
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
Helical Reconstruction with EmIP HelicalReconstruction
Processing - electron crystallography CemProtocProcessEC
Processing - tomographic data CemProtocProcessET
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Processing - Single particle analysis CemProtocProcessSPA
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

CEM Facility

CEM Newletter Archive NewsLetter
Facility Announcements CEMAnnouncements

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub


General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. All mirrored sites can be found on: CemTwikiToWebList. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact the CEM staff.

  • Set ALLOWTOPICVIEW =

Revision 2819 Dec 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"

Overview

Interested in Cryoem? (How to begin a project) CemInterested
Cryoem at NYSBC CemIntroduction
General info on cryoem at NYSBC CemGeneralInfo
Cryoem Operations committee CemOpCom
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
Added:
>
>
Overview of negatively-staining proteins for EM CemNegativeStain
 
How to sign up for CEM equipment at NYSBC CemSignupOverview
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
Publications related to CEM at NYSBC CemPublications
CEM Newsletter NewsLetter
The site map you are now viewing CemSiteMap

Equipment

Equipment overview - Sample preparation CemSamplePrep

Plasma cleaners

Plasma cleaners CemPlasmaCleaning
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
Glow Discharge Using Edwards Evaporator GlowDischarge

Cryo

Plunge freezing equipment CemPlungeFreezer
High Pressure Freezing Menu HighPressFreezer
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
Use of the Oscilloscope/ Matlab MatlabOscilloscope
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Main page for all Microscopes CryoEM
Microscope overview page CemMicroscopes
CEM Parameters CemParameters
How to Find The Beam FindBeam
Microscope Shut Down ShutDown

Jeol 1230

Jeol 1230 description Jeol1230Description
Jeol 1230 Information Jeol1230Information
Jeol 1230 Instructions Jeol1230Instructions
Jeo l1230 filament exchange instructions FilamentExchange

Jeol 2100

Jeol 2100 description Jeol2100Description
Jeol 2100 Information Jeol2100Information
Jeol 2100 Basic Instructions Jeol2100Basicinstructions
Jeol 2100 Instructions Jeol2100Instructions

Jeol 3200

Jeol 3200 description Jeol3200Description
Jeol 3200 Information Jeol3200Information
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
Tecnai Information TecnaiInformation
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
Tecnai Instructions TecnaiInstructions
Tecnai advanced instructions TecnaiAdvanced
Ccd Blank Enable, specific for Tecnai F20 CcdBlankEnable
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

FEI Helios Dual Beam overview HeliosDescription
Helios Instructions CemHeliosInstructions

Light Microscope

Nikon Eclipse Ti-U CemNikonEclipse
Basic Instructions for Nikon Ti-U NikonTiInstructions
How to deal with uneven grid? NikonTiFocusSurface

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage

Automated Data Collection

Automated data collection with Serial EM SerialEM
Older notes on Serial EM SerialEmNotes
Serial EM Macros SerialEMMacros
Notes on Shutter Box settings on Tecnai on Low Dose and Serial EM ShutterBox
Serial EM - notes on montages and use of the Navigator MontageNavigator
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList

Film Related

Film Screening And Scanning Overview FilmScreeningAndScanning
Scanning - PDS Densitometer PdsDensitometer
Scanning - Zeiss Densitometer ZeissDensitometer
Screening films with Optical Bench OpticalBench

Lab Protocols

Main protocols page CemProtoc

Grid Preparation

Grid prep - general information CemProtocGrids
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
Plastic Coated Grid PlasticCoatedGrid
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Considerations for electron tomography sample preperation CemProtocET
Fiducial Markers for Tomography PPFiducialsTomography
Carbon Coating instructions CarbonCoating
Carbon Coating using Thread CarbonThread
Carbon Coating using Carbon Rod CarbonRod
Metal Shadowing MetalShadowing
Rotary Shadowing CemRotaryShadowing

Staining

Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining

Cryo

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
High pressure freezing CemProtocHPFU
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc

Image Processing

Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
EmIP - How to Plot 1D CTF profile of an image FileConversion
Helical Processing : Initial steps HelicalProcessing
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
Helical Reconstruction with EmIP HelicalReconstruction
Processing - electron crystallography CemProtocProcessEC
Processing - tomographic data CemProtocProcessET
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Processing - Single particle analysis CemProtocProcessSPA
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

CEM Facility

CEM Newletter Archive NewsLetter
Facility Announcements CEMAnnouncements

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub


General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. All mirrored sites can be found on: CemTwikiToWebList. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact the CEM staff.

  • Set ALLOWTOPICVIEW =

Revision 2719 Dec 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"

Overview

Interested in Cryoem? (How to begin a project) CemInterested
Cryoem at NYSBC CemIntroduction
General info on cryoem at NYSBC CemGeneralInfo
Cryoem Operations committee CemOpCom
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
How to sign up for CEM equipment at NYSBC CemSignupOverview
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
Publications related to CEM at NYSBC CemPublications
CEM Newsletter NewsLetter
The site map you are now viewing CemSiteMap

Equipment

Equipment overview - Sample preparation CemSamplePrep

Plasma cleaners

Plasma cleaners CemPlasmaCleaning
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
Glow Discharge Using Edwards Evaporator GlowDischarge

Cryo

Plunge freezing equipment CemPlungeFreezer
High Pressure Freezing Menu HighPressFreezer
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
Use of the Oscilloscope/ Matlab MatlabOscilloscope
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Main page for all Microscopes CryoEM
Microscope overview page CemMicroscopes
CEM Parameters CemParameters
How to Find The Beam FindBeam
Microscope Shut Down ShutDown

Jeol 1230

Jeol 1230 description Jeol1230Description
Jeol 1230 Information Jeol1230Information
Jeol 1230 Instructions Jeol1230Instructions
Jeo l1230 filament exchange instructions FilamentExchange

Jeol 2100

Jeol 2100 description Jeol2100Description
Jeol 2100 Information Jeol2100Information
Jeol 2100 Basic Instructions Jeol2100Basicinstructions
Jeol 2100 Instructions Jeol2100Instructions

Jeol 3200

Jeol 3200 description Jeol3200Description
Jeol 3200 Information Jeol3200Information
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
Tecnai Information TecnaiInformation
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
Tecnai Instructions TecnaiInstructions
Tecnai advanced instructions TecnaiAdvanced
Ccd Blank Enable, specific for Tecnai F20 CcdBlankEnable
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

FEI Helios Dual Beam overview HeliosDescription
Helios Instructions CemHeliosInstructions

Light Microscope

Nikon Eclipse Ti-U CemNikonEclipse
Basic Instructions for Nikon Ti-U NikonTiInstructions
How to deal with uneven grid? NikonTiFocusSurface

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage

Automated Data Collection

Automated data collection with Serial EM SerialEM
Older notes on Serial EM SerialEmNotes
Serial EM Macros SerialEMMacros
Notes on Shutter Box settings on Tecnai on Low Dose and Serial EM ShutterBox
Serial EM - notes on montages and use of the Navigator MontageNavigator
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList

Film Related

Film Screening And Scanning Overview FilmScreeningAndScanning
Scanning - PDS Densitometer PdsDensitometer
Scanning - Zeiss Densitometer ZeissDensitometer
Screening films with Optical Bench OpticalBench

Lab Protocols

Main protocols page CemProtoc

Grid Preparation

Grid prep - general information CemProtocGrids
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
Plastic Coated Grid PlasticCoatedGrid
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Considerations for electron tomography sample preperation CemProtocET
Fiducial Markers for Tomography PPFiducialsTomography
Carbon Coating instructions CarbonCoating
Carbon Coating using Thread CarbonThread
Carbon Coating using Carbon Rod CarbonRod
Metal Shadowing MetalShadowing
Added:
>
>
Rotary Shadowing CemRotaryShadowing
 

Staining

Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining

Cryo

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
High pressure freezing CemProtocHPFU
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc

Image Processing

Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
EmIP - How to Plot 1D CTF profile of an image FileConversion
Helical Processing : Initial steps HelicalProcessing
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
Helical Reconstruction with EmIP HelicalReconstruction
Processing - electron crystallography CemProtocProcessEC
Processing - tomographic data CemProtocProcessET
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Processing - Single particle analysis CemProtocProcessSPA
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

CEM Facility

CEM Newletter Archive NewsLetter
Facility Announcements CEMAnnouncements

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub


General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. All mirrored sites can be found on: CemTwikiToWebList. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact the CEM staff.

  • Set ALLOWTOPICVIEW =

Revision 2620 Sep 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"

Overview

Interested in Cryoem? (How to begin a project) CemInterested
Cryoem at NYSBC CemIntroduction
General info on cryoem at NYSBC CemGeneralInfo
Cryoem Operations committee CemOpCom
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
How to sign up for CEM equipment at NYSBC CemSignupOverview
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
Publications related to CEM at NYSBC CemPublications
CEM Newsletter NewsLetter
The site map you are now viewing CemSiteMap

Equipment

Equipment overview - Sample preparation CemSamplePrep

Plasma cleaners

Plasma cleaners CemPlasmaCleaning
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
Glow Discharge Using Edwards Evaporator GlowDischarge

Cryo

Plunge freezing equipment CemPlungeFreezer
High Pressure Freezing Menu HighPressFreezer
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
Use of the Oscilloscope/ Matlab MatlabOscilloscope
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Main page for all Microscopes CryoEM
Microscope overview page CemMicroscopes
CEM Parameters CemParameters
How to Find The Beam FindBeam
Microscope Shut Down ShutDown

Jeol 1230

Jeol 1230 description Jeol1230Description
Jeol 1230 Information Jeol1230Information
Jeol 1230 Instructions Jeol1230Instructions
Jeo l1230 filament exchange instructions FilamentExchange

Jeol 2100

Jeol 2100 description Jeol2100Description
Jeol 2100 Information Jeol2100Information
Jeol 2100 Basic Instructions Jeol2100Basicinstructions
Jeol 2100 Instructions Jeol2100Instructions

Jeol 3200

Jeol 3200 description Jeol3200Description
Jeol 3200 Information Jeol3200Information
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
Tecnai Information TecnaiInformation
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
Tecnai Instructions TecnaiInstructions
Tecnai advanced instructions TecnaiAdvanced
Ccd Blank Enable, specific for Tecnai F20 CcdBlankEnable
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

FEI Helios Dual Beam overview HeliosDescription
Helios Instructions CemHeliosInstructions

Light Microscope

Nikon Eclipse Ti-U CemNikonEclipse
Added:
>
>
Basic Instructions for Nikon Ti-U NikonTiInstructions
How to deal with uneven grid? NikonTiFocusSurface
 

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage

Automated Data Collection

Automated data collection with Serial EM SerialEM
Older notes on Serial EM SerialEmNotes
Serial EM Macros SerialEMMacros
Notes on Shutter Box settings on Tecnai on Low Dose and Serial EM ShutterBox
Serial EM - notes on montages and use of the Navigator MontageNavigator
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList

Film Related

Film Screening And Scanning Overview FilmScreeningAndScanning
Scanning - PDS Densitometer PdsDensitometer
Scanning - Zeiss Densitometer ZeissDensitometer
Screening films with Optical Bench OpticalBench

Lab Protocols

Main protocols page CemProtoc

Grid Preparation

Grid prep - general information CemProtocGrids
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
Plastic Coated Grid PlasticCoatedGrid
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Considerations for electron tomography sample preperation CemProtocET
Fiducial Markers for Tomography PPFiducialsTomography
Carbon Coating instructions CarbonCoating
Carbon Coating using Thread CarbonThread
Carbon Coating using Carbon Rod CarbonRod
Metal Shadowing MetalShadowing

Staining

Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining

Cryo

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
High pressure freezing CemProtocHPFU
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc

Image Processing

Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
EmIP - How to Plot 1D CTF profile of an image FileConversion
Helical Processing : Initial steps HelicalProcessing
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
Helical Reconstruction with EmIP HelicalReconstruction
Processing - electron crystallography CemProtocProcessEC
Processing - tomographic data CemProtocProcessET
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Processing - Single particle analysis CemProtocProcessSPA
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

CEM Facility

CEM Newletter Archive NewsLetter
Facility Announcements CEMAnnouncements

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub


General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. All mirrored sites can be found on: CemTwikiToWebList. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact the CEM staff.

  • Set ALLOWTOPICVIEW =

Revision 2530 Aug 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"

Deleted:
<
<
Contents
 

Overview

Interested in Cryoem? (How to begin a project) CemInterested
Cryoem at NYSBC CemIntroduction
General info on cryoem at NYSBC CemGeneralInfo
Cryoem Operations committee CemOpCom
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
How to sign up for CEM equipment at NYSBC CemSignupOverview
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
Publications related to CEM at NYSBC CemPublications
CEM Newsletter NewsLetter
The site map you are now viewing CemSiteMap

Equipment

Equipment overview - Sample preparation CemSamplePrep

Plasma cleaners

Plasma cleaners CemPlasmaCleaning
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
Glow Discharge Using Edwards Evaporator GlowDischarge

Cryo

Plunge freezing equipment CemPlungeFreezer
High Pressure Freezing Menu HighPressFreezer
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
Use of the Oscilloscope/ Matlab MatlabOscilloscope
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Main page for all Microscopes CryoEM
Microscope overview page CemMicroscopes
CEM Parameters CemParameters
How to Find The Beam FindBeam
Microscope Shut Down ShutDown

Jeol 1230

Jeol 1230 description Jeol1230Description
Jeol 1230 Information Jeol1230Information
Jeol 1230 Instructions Jeol1230Instructions
Jeo l1230 filament exchange instructions FilamentExchange

Jeol 2100

Jeol 2100 description Jeol2100Description
Jeol 2100 Information Jeol2100Information
Jeol 2100 Basic Instructions Jeol2100Basicinstructions
Jeol 2100 Instructions Jeol2100Instructions

Jeol 3200

Jeol 3200 description Jeol3200Description
Jeol 3200 Information Jeol3200Information
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
Tecnai Information TecnaiInformation
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
Tecnai Instructions TecnaiInstructions
Tecnai advanced instructions TecnaiAdvanced
Ccd Blank Enable, specific for Tecnai F20 CcdBlankEnable
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

FEI Helios Dual Beam overview HeliosDescription
Helios Instructions CemHeliosInstructions

Light Microscope

Nikon Eclipse Ti-U CemNikonEclipse

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage

Automated Data Collection

Automated data collection with Serial EM SerialEM
Older notes on Serial EM SerialEmNotes
Serial EM Macros SerialEMMacros
Notes on Shutter Box settings on Tecnai on Low Dose and Serial EM ShutterBox
Serial EM - notes on montages and use of the Navigator MontageNavigator
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList

Film Related

Film Screening And Scanning Overview FilmScreeningAndScanning
Scanning - PDS Densitometer PdsDensitometer
Scanning - Zeiss Densitometer ZeissDensitometer
Screening films with Optical Bench OpticalBench

Lab Protocols

Main protocols page CemProtoc

Grid Preparation

Grid prep - general information CemProtocGrids
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
Plastic Coated Grid PlasticCoatedGrid
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Considerations for electron tomography sample preperation CemProtocET
Fiducial Markers for Tomography PPFiducialsTomography
Carbon Coating instructions CarbonCoating
Carbon Coating using Thread CarbonThread
Carbon Coating using Carbon Rod CarbonRod
Metal Shadowing MetalShadowing

Staining

Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining

Cryo

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
High pressure freezing CemProtocHPFU
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc

Image Processing

Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
EmIP - How to Plot 1D CTF profile of an image FileConversion
Helical Processing : Initial steps HelicalProcessing
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
Helical Reconstruction with EmIP HelicalReconstruction
Processing - electron crystallography CemProtocProcessEC
Processing - tomographic data CemProtocProcessET
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Processing - Single particle analysis CemProtocProcessSPA
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

CEM Facility

CEM Newletter Archive NewsLetter
Facility Announcements CEMAnnouncements

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub


General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. All mirrored sites can be found on: CemTwikiToWebList. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact the CEM staff.

  • Set ALLOWTOPICVIEW =
Deleted:
<
<

Revision 2424 Jul 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"

Contents

Overview

Interested in Cryoem? (How to begin a project) CemInterested
Cryoem at NYSBC CemIntroduction
General info on cryoem at NYSBC CemGeneralInfo
Cryoem Operations committee CemOpCom
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
How to sign up for CEM equipment at NYSBC CemSignupOverview
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
Publications related to CEM at NYSBC CemPublications
CEM Newsletter NewsLetter
The site map you are now viewing CemSiteMap

Equipment

Equipment overview - Sample preparation CemSamplePrep

Plasma cleaners

Plasma cleaners CemPlasmaCleaning
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
Glow Discharge Using Edwards Evaporator GlowDischarge

Cryo

Plunge freezing equipment CemPlungeFreezer
High Pressure Freezing Menu HighPressFreezer
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
Use of the Oscilloscope/ Matlab MatlabOscilloscope
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Main page for all Microscopes CryoEM
Microscope overview page CemMicroscopes
CEM Parameters CemParameters
How to Find The Beam FindBeam
Microscope Shut Down ShutDown

Jeol 1230

Jeol 1230 description Jeol1230Description
Jeol 1230 Information Jeol1230Information
Jeol 1230 Instructions Jeol1230Instructions
Jeo l1230 filament exchange instructions FilamentExchange

Jeol 2100

Jeol 2100 description Jeol2100Description
Jeol 2100 Information Jeol2100Information
Jeol 2100 Basic Instructions Jeol2100Basicinstructions
Jeol 2100 Instructions Jeol2100Instructions

Jeol 3200

Jeol 3200 description Jeol3200Description
Jeol 3200 Information Jeol3200Information
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
Tecnai Information TecnaiInformation
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
Tecnai Instructions TecnaiInstructions
Tecnai advanced instructions TecnaiAdvanced
Ccd Blank Enable, specific for Tecnai F20 CcdBlankEnable
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

FEI Helios Dual Beam overview HeliosDescription
Helios Instructions CemHeliosInstructions

Light Microscope

Nikon Eclipse Ti-U CemNikonEclipse

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage

Automated Data Collection

Automated data collection with Serial EM SerialEM
Older notes on Serial EM SerialEmNotes
Serial EM Macros SerialEMMacros
Notes on Shutter Box settings on Tecnai on Low Dose and Serial EM ShutterBox
Serial EM - notes on montages and use of the Navigator MontageNavigator
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList

Film Related

Film Screening And Scanning Overview FilmScreeningAndScanning
Scanning - PDS Densitometer PdsDensitometer
Scanning - Zeiss Densitometer ZeissDensitometer
Screening films with Optical Bench OpticalBench

Lab Protocols

Main protocols page CemProtoc

Grid Preparation

Grid prep - general information CemProtocGrids
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
Plastic Coated Grid PlasticCoatedGrid
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Considerations for electron tomography sample preperation CemProtocET
Fiducial Markers for Tomography PPFiducialsTomography
Carbon Coating instructions CarbonCoating
Carbon Coating using Thread CarbonThread
Carbon Coating using Carbon Rod CarbonRod
Metal Shadowing MetalShadowing

Staining

Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining

Cryo

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
High pressure freezing CemProtocHPFU
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc

Image Processing

Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
EmIP - How to Plot 1D CTF profile of an image FileConversion
Helical Processing : Initial steps HelicalProcessing
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
Helical Reconstruction with EmIP HelicalReconstruction
Processing - electron crystallography CemProtocProcessEC
Processing - tomographic data CemProtocProcessET
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Processing - Single particle analysis CemProtocProcessSPA
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie
Added:
>
>

CEM Facility

CEM Newletter Archive NewsLetter
Facility Announcements CEMAnnouncements
 

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub


General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. All mirrored sites can be found on: CemTwikiToWebList. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact the CEM staff.

  • Set ALLOWTOPICVIEW =

Revision 2311 Jul 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Added:
>
>

 Contents

Overview

Interested in Cryoem? (How to begin a project) CemInterested
Cryoem at NYSBC CemIntroduction
General info on cryoem at NYSBC CemGeneralInfo
Cryoem Operations committee CemOpCom
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
How to sign up for CEM equipment at NYSBC CemSignupOverview
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
Publications related to CEM at NYSBC CemPublications
Added:
>
>
CEM Newsletter NewsLetter
 
The site map you are now viewing CemSiteMap

Equipment

Equipment overview - Sample preparation CemSamplePrep

Plasma cleaners

Plasma cleaners CemPlasmaCleaning
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
Glow Discharge Using Edwards Evaporator GlowDischarge

Cryo

Plunge freezing equipment CemPlungeFreezer
High Pressure Freezing Menu HighPressFreezer
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
Use of the Oscilloscope/ Matlab MatlabOscilloscope
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Main page for all Microscopes CryoEM
Microscope overview page CemMicroscopes
CEM Parameters CemParameters
How to Find The Beam FindBeam
Microscope Shut Down ShutDown

Jeol 1230

Jeol 1230 description Jeol1230Description
Jeol 1230 Information Jeol1230Information
Jeol 1230 Instructions Jeol1230Instructions
Jeo l1230 filament exchange instructions FilamentExchange

Jeol 2100

Jeol 2100 description Jeol2100Description
Jeol 2100 Information Jeol2100Information
Jeol 2100 Basic Instructions Jeol2100Basicinstructions
Jeol 2100 Instructions Jeol2100Instructions

Jeol 3200

Jeol 3200 description Jeol3200Description
Jeol 3200 Information Jeol3200Information
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
Tecnai Information TecnaiInformation
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
Tecnai Instructions TecnaiInstructions
Tecnai advanced instructions TecnaiAdvanced
Ccd Blank Enable, specific for Tecnai F20 CcdBlankEnable
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

FEI Helios Dual Beam overview HeliosDescription
Helios Instructions CemHeliosInstructions

Light Microscope

Nikon Eclipse Ti-U CemNikonEclipse

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage

Automated Data Collection

Automated data collection with Serial EM SerialEM
Older notes on Serial EM SerialEmNotes
Serial EM Macros SerialEMMacros
Notes on Shutter Box settings on Tecnai on Low Dose and Serial EM ShutterBox
Serial EM - notes on montages and use of the Navigator MontageNavigator
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList

Film Related

Film Screening And Scanning Overview FilmScreeningAndScanning
Scanning - PDS Densitometer PdsDensitometer
Scanning - Zeiss Densitometer ZeissDensitometer
Screening films with Optical Bench OpticalBench

Lab Protocols

Main protocols page CemProtoc

Grid Preparation

Grid prep - general information CemProtocGrids
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
Plastic Coated Grid PlasticCoatedGrid
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Considerations for electron tomography sample preperation CemProtocET
Fiducial Markers for Tomography PPFiducialsTomography
Carbon Coating instructions CarbonCoating
Carbon Coating using Thread CarbonThread
Carbon Coating using Carbon Rod CarbonRod
Metal Shadowing MetalShadowing

Staining

Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining

Cryo

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
High pressure freezing CemProtocHPFU
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc

Image Processing

Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
EmIP - How to Plot 1D CTF profile of an image FileConversion
Helical Processing : Initial steps HelicalProcessing
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
Helical Reconstruction with EmIP HelicalReconstruction
Processing - electron crystallography CemProtocProcessEC
Processing - tomographic data CemProtocProcessET
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Processing - Single particle analysis CemProtocProcessSPA
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub


General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. All mirrored sites can be found on: CemTwikiToWebList. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact the CEM staff.

  • Set ALLOWTOPICVIEW =
Deleted:
<
<
-- EdEng - 17 May 2012

Revision 2227 Jun 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Contents

Overview

Interested in Cryoem? (How to begin a project) CemInterested
Cryoem at NYSBC CemIntroduction
General info on cryoem at NYSBC CemGeneralInfo
Cryoem Operations committee CemOpCom
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
How to sign up for CEM equipment at NYSBC CemSignupOverview
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
Publications related to CEM at NYSBC CemPublications
The site map you are now viewing CemSiteMap

Equipment

Equipment overview - Sample preparation CemSamplePrep

Plasma cleaners

Plasma cleaners CemPlasmaCleaning
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
Glow Discharge Using Edwards Evaporator GlowDischarge

Cryo

Plunge freezing equipment CemPlungeFreezer
High Pressure Freezing Menu HighPressFreezer
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
Use of the Oscilloscope/ Matlab MatlabOscilloscope
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Main page for all Microscopes CryoEM
Microscope overview page CemMicroscopes
CEM Parameters CemParameters
How to Find The Beam FindBeam
Microscope Shut Down ShutDown

Jeol 1230

Jeol 1230 description Jeol1230Description
Jeol 1230 Information Jeol1230Information
Jeol 1230 Instructions Jeol1230Instructions
Jeo l1230 filament exchange instructions FilamentExchange

Jeol 2100

Jeol 2100 description Jeol2100Description
Jeol 2100 Information Jeol2100Information
Jeol 2100 Basic Instructions Jeol2100Basicinstructions
Jeol 2100 Instructions Jeol2100Instructions

Jeol 3200

Jeol 3200 description Jeol3200Description
Jeol 3200 Information Jeol3200Information
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
Tecnai Information TecnaiInformation
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
Tecnai Instructions TecnaiInstructions
Tecnai advanced instructions TecnaiAdvanced
Ccd Blank Enable, specific for Tecnai F20 CcdBlankEnable
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

FEI Helios Dual Beam overview HeliosDescription
Helios Instructions CemHeliosInstructions
Added:
>
>

Light Microscope

Nikon Eclipse Ti-U CemNikonEclipse
 

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage

Automated Data Collection

Automated data collection with Serial EM SerialEM
Older notes on Serial EM SerialEmNotes
Serial EM Macros SerialEMMacros
Notes on Shutter Box settings on Tecnai on Low Dose and Serial EM ShutterBox
Serial EM - notes on montages and use of the Navigator MontageNavigator
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList

Film Related

Film Screening And Scanning Overview FilmScreeningAndScanning
Scanning - PDS Densitometer PdsDensitometer
Scanning - Zeiss Densitometer ZeissDensitometer
Screening films with Optical Bench OpticalBench

Lab Protocols

Main protocols page CemProtoc

Grid Preparation

Grid prep - general information CemProtocGrids
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
Plastic Coated Grid PlasticCoatedGrid
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Considerations for electron tomography sample preperation CemProtocET
Fiducial Markers for Tomography PPFiducialsTomography
Carbon Coating instructions CarbonCoating
Carbon Coating using Thread CarbonThread
Carbon Coating using Carbon Rod CarbonRod
Metal Shadowing MetalShadowing

Staining

Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining

Cryo

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
High pressure freezing CemProtocHPFU
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc

Image Processing

Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
EmIP - How to Plot 1D CTF profile of an image FileConversion
Helical Processing : Initial steps HelicalProcessing
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
Helical Reconstruction with EmIP HelicalReconstruction
Processing - electron crystallography CemProtocProcessEC
Processing - tomographic data CemProtocProcessET
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Processing - Single particle analysis CemProtocProcessSPA
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub


General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. All mirrored sites can be found on: CemTwikiToWebList. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact the CEM staff.

  • Set ALLOWTOPICVIEW =

-- EdEng - 17 May 2012

Revision 2120 Jun 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Contents

Overview

Interested in Cryoem? (How to begin a project) CemInterested
Cryoem at NYSBC CemIntroduction
General info on cryoem at NYSBC CemGeneralInfo
Cryoem Operations committee CemOpCom
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
How to sign up for CEM equipment at NYSBC CemSignupOverview
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
Publications related to CEM at NYSBC CemPublications
The site map you are now viewing CemSiteMap

Equipment

Equipment overview - Sample preparation CemSamplePrep

Plasma cleaners

Plasma cleaners CemPlasmaCleaning
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
Glow Discharge Using Edwards Evaporator GlowDischarge

Cryo

Plunge freezing equipment CemPlungeFreezer
High Pressure Freezing Menu HighPressFreezer
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
Use of the Oscilloscope/ Matlab MatlabOscilloscope
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Main page for all Microscopes CryoEM
Microscope overview page CemMicroscopes
CEM Parameters CemParameters
How to Find The Beam FindBeam
Microscope Shut Down ShutDown

Jeol 1230

Jeol 1230 description Jeol1230Description
Jeol 1230 Information Jeol1230Information
Jeol 1230 Instructions Jeol1230Instructions
Jeo l1230 filament exchange instructions FilamentExchange

Jeol 2100

Jeol 2100 description Jeol2100Description
Jeol 2100 Information Jeol2100Information
Jeol 2100 Basic Instructions Jeol2100Basicinstructions
Jeol 2100 Instructions Jeol2100Instructions

Jeol 3200

Jeol 3200 description Jeol3200Description
Changed:
<
<
Jeol 3200Information Jeol3200Information
>
>
Jeol 3200 Information Jeol3200Information
 
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
Tecnai Information TecnaiInformation
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
Tecnai Instructions TecnaiInstructions
Tecnai advanced instructions TecnaiAdvanced
Ccd Blank Enable, specific for Tecnai F20 CcdBlankEnable
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

FEI Helios Dual Beam overview HeliosDescription
Helios Instructions CemHeliosInstructions

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage

Automated Data Collection

Automated data collection with Serial EM SerialEM
Older notes on Serial EM SerialEmNotes
Serial EM Macros SerialEMMacros
Notes on Shutter Box settings on Tecnai on Low Dose and Serial EM ShutterBox
Serial EM - notes on montages and use of the Navigator MontageNavigator
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList

Film Related

Film Screening And Scanning Overview FilmScreeningAndScanning
Scanning - PDS Densitometer PdsDensitometer
Scanning - Zeiss Densitometer ZeissDensitometer
Screening films with Optical Bench OpticalBench

Lab Protocols

Main protocols page CemProtoc

Grid Preparation

Grid prep - general information CemProtocGrids
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
Plastic Coated Grid PlasticCoatedGrid
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Considerations for electron tomography sample preperation CemProtocET
Fiducial Markers for Tomography PPFiducialsTomography
Carbon Coating instructions CarbonCoating
Carbon Coating using Thread CarbonThread
Carbon Coating using Carbon Rod CarbonRod
Metal Shadowing MetalShadowing

Staining

Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining

Cryo

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
High pressure freezing CemProtocHPFU
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc

Image Processing

Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
EmIP - How to Plot 1D CTF profile of an image FileConversion
Helical Processing : Initial steps HelicalProcessing
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
Helical Reconstruction with EmIP HelicalReconstruction
Processing - electron crystallography CemProtocProcessEC
Processing - tomographic data CemProtocProcessET
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Processing - Single particle analysis CemProtocProcessSPA
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub


General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. All mirrored sites can be found on: CemTwikiToWebList. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact the CEM staff.

  • Set ALLOWTOPICVIEW =

-- EdEng - 17 May 2012

Revision 2007 Jun 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Contents

Overview

Interested in Cryoem? (How to begin a project) CemInterested
Cryoem at NYSBC CemIntroduction
General info on cryoem at NYSBC CemGeneralInfo
Cryoem Operations committee CemOpCom
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
How to sign up for CEM equipment at NYSBC CemSignupOverview
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
Publications related to CEM at NYSBC CemPublications
The site map you are now viewing CemSiteMap

Equipment

Equipment overview - Sample preparation CemSamplePrep

Plasma cleaners

Plasma cleaners CemPlasmaCleaning
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
Glow Discharge Using Edwards Evaporator GlowDischarge

Cryo

Plunge freezing equipment CemPlungeFreezer
High Pressure Freezing Menu HighPressFreezer
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
Use of the Oscilloscope/ Matlab MatlabOscilloscope
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Main page for all Microscopes CryoEM
Microscope overview page CemMicroscopes
CEM Parameters CemParameters
How to Find The Beam FindBeam
Microscope Shut Down ShutDown

Jeol 1230

Jeol 1230 description Jeol1230Description
Jeol 1230 Information Jeol1230Information
Jeol 1230 Instructions Jeol1230Instructions
Jeo l1230 filament exchange instructions FilamentExchange

Jeol 2100

Jeol 2100 description Jeol2100Description
Jeol 2100 Information Jeol2100Information
Jeol 2100 Basic Instructions Jeol2100Basicinstructions
Jeol 2100 Instructions Jeol2100Instructions

Jeol 3200

Jeol 3200 description Jeol3200Description
Jeol 3200Information Jeol3200Information
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
Tecnai Information TecnaiInformation
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
Tecnai Instructions TecnaiInstructions
Tecnai advanced instructions TecnaiAdvanced
Ccd Blank Enable, specific for Tecnai F20 CcdBlankEnable
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

FEI Helios Dual Beam overview HeliosDescription
Helios Instructions CemHeliosInstructions

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage

Automated Data Collection

Automated data collection with Serial EM SerialEM
Older notes on Serial EM SerialEmNotes
Serial EM Macros SerialEMMacros
Notes on Shutter Box settings on Tecnai on Low Dose and Serial EM ShutterBox
Serial EM - notes on montages and use of the Navigator MontageNavigator
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList

Film Related

Film Screening And Scanning Overview FilmScreeningAndScanning
Scanning - PDS Densitometer PdsDensitometer
Scanning - Zeiss Densitometer ZeissDensitometer
Screening films with Optical Bench OpticalBench

Lab Protocols

Main protocols page CemProtoc

Grid Preparation

Grid prep - general information CemProtocGrids
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
Plastic Coated Grid PlasticCoatedGrid
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Considerations for electron tomography sample preperation CemProtocET
Fiducial Markers for Tomography PPFiducialsTomography
Carbon Coating instructions CarbonCoating
Carbon Coating using Thread CarbonThread
Carbon Coating using Carbon Rod CarbonRod
Metal Shadowing MetalShadowing

Staining

Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining

Cryo

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
High pressure freezing CemProtocHPFU
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc

Image Processing

Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
EmIP - How to Plot 1D CTF profile of an image FileConversion
Helical Processing : Initial steps HelicalProcessing
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
Helical Reconstruction with EmIP HelicalReconstruction
Processing - electron crystallography CemProtocProcessEC
Processing - tomographic data CemProtocProcessET
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Processing - Single particle analysis CemProtocProcessSPA
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub


General info about this sitemap

Changed:
<
<
This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. All mirrored sites can be found on: CemTwikiToWebListTest. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact the CEM staff.
>
>
This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. All mirrored sites can be found on: CemTwikiToWebList. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact the CEM staff.
 

  • Set ALLOWTOPICVIEW =

-- EdEng - 17 May 2012

Deleted:
<
<

Revision 1918 May 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Contents

Overview

Interested in Cryoem? (How to begin a project) CemInterested
Cryoem at NYSBC CemIntroduction
General info on cryoem at NYSBC CemGeneralInfo
Cryoem Operations committee CemOpCom
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
How to sign up for CEM equipment at NYSBC CemSignupOverview
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
Publications related to CEM at NYSBC CemPublications
The site map you are now viewing CemSiteMap

Equipment

Equipment overview - Sample preparation CemSamplePrep

Plasma cleaners

Plasma cleaners CemPlasmaCleaning
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
Glow Discharge Using Edwards Evaporator GlowDischarge

Cryo

Changed:
<
<
CemPlungeFreezer?
>
>
Plunge freezing equipment CemPlungeFreezer
 
High Pressure Freezing Menu HighPressFreezer
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
Use of the Oscilloscope/ Matlab MatlabOscilloscope
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Main page for all Microscopes CryoEM
Microscope overview page CemMicroscopes
CEM Parameters CemParameters
How to Find The Beam FindBeam
Microscope Shut Down ShutDown

Jeol 1230

Jeol 1230 description Jeol1230Description
Jeol 1230 Information Jeol1230Information
Jeol 1230 Instructions Jeol1230Instructions
Jeo l1230 filament exchange instructions FilamentExchange

Jeol 2100

Jeol 2100 description Jeol2100Description
Jeol 2100 Information Jeol2100Information
Jeol 2100 Basic Instructions Jeol2100Basicinstructions
Jeol 2100 Instructions Jeol2100Instructions

Jeol 3200

Jeol 3200 description Jeol3200Description
Jeol 3200Information Jeol3200Information
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
Tecnai Information TecnaiInformation
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
Tecnai Instructions TecnaiInstructions
Tecnai advanced instructions TecnaiAdvanced
Ccd Blank Enable, specific for Tecnai F20 CcdBlankEnable
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

FEI Helios Dual Beam overview HeliosDescription
Helios Instructions CemHeliosInstructions

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage

Automated Data Collection

Automated data collection with Serial EM SerialEM
Older notes on Serial EM SerialEmNotes
Serial EM Macros SerialEMMacros
Notes on Shutter Box settings on Tecnai on Low Dose and Serial EM ShutterBox
Serial EM - notes on montages and use of the Navigator MontageNavigator
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList

Film Related

Film Screening And Scanning Overview FilmScreeningAndScanning
Scanning - PDS Densitometer PdsDensitometer
Scanning - Zeiss Densitometer ZeissDensitometer
Screening films with Optical Bench OpticalBench

Lab Protocols

Main protocols page CemProtoc

Grid Preparation

Grid prep - general information CemProtocGrids
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
Plastic Coated Grid PlasticCoatedGrid
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Considerations for electron tomography sample preperation CemProtocET
Fiducial Markers for Tomography PPFiducialsTomography
Carbon Coating instructions CarbonCoating
Carbon Coating using Thread CarbonThread
Carbon Coating using Carbon Rod CarbonRod
Metal Shadowing MetalShadowing

Staining

Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining

Cryo

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
High pressure freezing CemProtocHPFU
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc

Image Processing

Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
EmIP - How to Plot 1D CTF profile of an image FileConversion
Helical Processing : Initial steps HelicalProcessing
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
Helical Reconstruction with EmIP HelicalReconstruction
Processing - electron crystallography CemProtocProcessEC
Processing - tomographic data CemProtocProcessET
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Processing - Single particle analysis CemProtocProcessSPA
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub


General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. All mirrored sites can be found on: CemTwikiToWebListTest. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact the CEM staff.

  • Set ALLOWTOPICVIEW =

-- EdEng - 17 May 2012

Added:
>
>

Revision 1818 May 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Contents

Overview

Interested in Cryoem? (How to begin a project) CemInterested
Cryoem at NYSBC CemIntroduction
General info on cryoem at NYSBC CemGeneralInfo
Cryoem Operations committee CemOpCom
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
How to sign up for CEM equipment at NYSBC CemSignupOverview
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
Publications related to CEM at NYSBC CemPublications
The site map you are now viewing CemSiteMap

Equipment

Equipment overview - Sample preparation CemSamplePrep

Plasma cleaners

Plasma cleaners CemPlasmaCleaning
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
Glow Discharge Using Edwards Evaporator GlowDischarge

Cryo

Changed:
<
<
Plunge freezing equipment CemPlungeFreezer
>
>
CemPlungeFreezer?
 
High Pressure Freezing Menu HighPressFreezer
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
Use of the Oscilloscope/ Matlab MatlabOscilloscope
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Main page for all Microscopes CryoEM
Microscope overview page CemMicroscopes
CEM Parameters CemParameters
How to Find The Beam FindBeam
Microscope Shut Down ShutDown

Jeol 1230

Jeol 1230 description Jeol1230Description
Jeol 1230 Information Jeol1230Information
Jeol 1230 Instructions Jeol1230Instructions
Jeo l1230 filament exchange instructions FilamentExchange

Jeol 2100

Jeol 2100 description Jeol2100Description
Jeol 2100 Information Jeol2100Information
Jeol 2100 Basic Instructions Jeol2100Basicinstructions
Jeol 2100 Instructions Jeol2100Instructions

Jeol 3200

Jeol 3200 description Jeol3200Description
Jeol 3200Information Jeol3200Information
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
Tecnai Information TecnaiInformation
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
Tecnai Instructions TecnaiInstructions
Tecnai advanced instructions TecnaiAdvanced
Ccd Blank Enable, specific for Tecnai F20 CcdBlankEnable
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

FEI Helios Dual Beam overview HeliosDescription
Helios Instructions CemHeliosInstructions

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage

Automated Data Collection

Automated data collection with Serial EM SerialEM
Older notes on Serial EM SerialEmNotes
Serial EM Macros SerialEMMacros
Notes on Shutter Box settings on Tecnai on Low Dose and Serial EM ShutterBox
Serial EM - notes on montages and use of the Navigator MontageNavigator
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList

Film Related

Film Screening And Scanning Overview FilmScreeningAndScanning
Scanning - PDS Densitometer PdsDensitometer
Scanning - Zeiss Densitometer ZeissDensitometer
Screening films with Optical Bench OpticalBench

Lab Protocols

Main protocols page CemProtoc

Grid Preparation

Grid prep - general information CemProtocGrids
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
Plastic Coated Grid PlasticCoatedGrid
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Considerations for electron tomography sample preperation CemProtocET
Fiducial Markers for Tomography PPFiducialsTomography
Carbon Coating instructions CarbonCoating
Carbon Coating using Thread CarbonThread
Carbon Coating using Carbon Rod CarbonRod
Metal Shadowing MetalShadowing

Staining

Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining

Cryo

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
High pressure freezing CemProtocHPFU
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc

Image Processing

Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
EmIP - How to Plot 1D CTF profile of an image FileConversion
Helical Processing : Initial steps HelicalProcessing
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
Helical Reconstruction with EmIP HelicalReconstruction
Processing - electron crystallography CemProtocProcessEC
Processing - tomographic data CemProtocProcessET
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Processing - Single particle analysis CemProtocProcessSPA
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub


General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. All mirrored sites can be found on: CemTwikiToWebListTest. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact the CEM staff.

  • Set ALLOWTOPICVIEW =

-- EdEng - 17 May 2012

Revision 1718 May 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Contents

Overview

Interested in Cryoem? (How to begin a project) CemInterested
Cryoem at NYSBC CemIntroduction
General info on cryoem at NYSBC CemGeneralInfo
Cryoem Operations committee CemOpCom
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
How to sign up for CEM equipment at NYSBC CemSignupOverview
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
Publications related to CEM at NYSBC CemPublications
The site map you are now viewing CemSiteMap

Equipment

Equipment overview - Sample preparation CemSamplePrep
Changed:
<
<

Plasma cleaners

>
>

Plasma cleaners

 
Plasma cleaners CemPlasmaCleaning
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
Glow Discharge Using Edwards Evaporator GlowDischarge
Changed:
<
<

Cryo

>
>

Cryo

 
Plunge freezing equipment CemPlungeFreezer
High Pressure Freezing Menu HighPressFreezer
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
Use of the Oscilloscope/ Matlab MatlabOscilloscope
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Main page for all Microscopes CryoEM
Microscope overview page CemMicroscopes
CEM Parameters CemParameters
How to Find The Beam FindBeam
Microscope Shut Down ShutDown

Jeol 1230

Jeol 1230 description Jeol1230Description
Jeol 1230 Information Jeol1230Information
Jeol 1230 Instructions Jeol1230Instructions
Jeo l1230 filament exchange instructions FilamentExchange

Jeol 2100

Jeol 2100 description Jeol2100Description
Jeol 2100 Information Jeol2100Information
Jeol 2100 Basic Instructions Jeol2100Basicinstructions
Jeol 2100 Instructions Jeol2100Instructions

Jeol 3200

Jeol 3200 description Jeol3200Description
Jeol 3200Information Jeol3200Information
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
Tecnai Information TecnaiInformation
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
Tecnai Instructions TecnaiInstructions
Tecnai advanced instructions TecnaiAdvanced
Ccd Blank Enable, specific for Tecnai F20 CcdBlankEnable
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

FEI Helios Dual Beam overview HeliosDescription
Helios Instructions CemHeliosInstructions

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage

Automated Data Collection

Automated data collection with Serial EM SerialEM
Older notes on Serial EM SerialEmNotes
Serial EM Macros SerialEMMacros
Notes on Shutter Box settings on Tecnai on Low Dose and Serial EM ShutterBox
Serial EM - notes on montages and use of the Navigator MontageNavigator
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList

Film Related

Film Screening And Scanning Overview FilmScreeningAndScanning
Scanning - PDS Densitometer PdsDensitometer
Scanning - Zeiss Densitometer ZeissDensitometer
Screening films with Optical Bench OpticalBench

Lab Protocols

Main protocols page CemProtoc

Grid Preparation

Grid prep - general information CemProtocGrids
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
Plastic Coated Grid PlasticCoatedGrid
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Considerations for electron tomography sample preperation CemProtocET
Fiducial Markers for Tomography PPFiducialsTomography
Carbon Coating instructions CarbonCoating
Carbon Coating using Thread CarbonThread
Carbon Coating using Carbon Rod CarbonRod
Metal Shadowing MetalShadowing

Staining

Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining

Cryo

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
High pressure freezing CemProtocHPFU
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc

Image Processing

Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
EmIP - How to Plot 1D CTF profile of an image FileConversion
Helical Processing : Initial steps HelicalProcessing
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
Helical Reconstruction with EmIP HelicalReconstruction
Processing - electron crystallography CemProtocProcessEC
Processing - tomographic data CemProtocProcessET
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Processing - Single particle analysis CemProtocProcessSPA
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub


General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. All mirrored sites can be found on: CemTwikiToWebListTest. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact the CEM staff.

  • Set ALLOWTOPICVIEW =

-- EdEng - 17 May 2012

Deleted:
<
<

Revision 1618 May 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Contents
Changed:
<
<
Overview  
>
>

Overview

 
Interested in Cryoem? (How to begin a project) CemInterested
Cryoem at NYSBC CemIntroduction
General info on cryoem at NYSBC CemGeneralInfo
Cryoem Operations committee CemOpCom
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
How to sign up for CEM equipment at NYSBC CemSignupOverview
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
Publications related to CEM at NYSBC CemPublications
The site map you are now viewing CemSiteMap
Changed:
<
<
Equipment  
>
>
Added:
>
>

Equipment

 
Equipment overview - Sample preparation CemSamplePrep
Changed:
<
<
Plasma cleaners  
>
>
Added:
>
>

Plasma cleaners

 
Plasma cleaners CemPlasmaCleaning
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
Glow Discharge Using Edwards Evaporator GlowDischarge
Changed:
<
<
Cryo  
>
>
Added:
>
>

Cryo

 
Plunge freezing equipment CemPlungeFreezer
High Pressure Freezing Menu HighPressFreezer
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
Use of the Oscilloscope/ Matlab MatlabOscilloscope
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Main page for all Microscopes CryoEM
Microscope overview page CemMicroscopes
CEM Parameters CemParameters
How to Find The Beam FindBeam
Microscope Shut Down ShutDown

Jeol 1230

Jeol 1230 description Jeol1230Description
Jeol 1230 Information Jeol1230Information
Jeol 1230 Instructions Jeol1230Instructions
Jeo l1230 filament exchange instructions FilamentExchange

Jeol 2100

Jeol 2100 description Jeol2100Description
Jeol 2100 Information Jeol2100Information
Jeol 2100 Basic Instructions Jeol2100Basicinstructions
Jeol 2100 Instructions Jeol2100Instructions

Jeol 3200

Jeol 3200 description Jeol3200Description
Jeol 3200Information Jeol3200Information
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
Tecnai Information TecnaiInformation
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
Tecnai Instructions TecnaiInstructions
Tecnai advanced instructions TecnaiAdvanced
Ccd Blank Enable, specific for Tecnai F20 CcdBlankEnable
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

FEI Helios Dual Beam overview HeliosDescription
Helios Instructions CemHeliosInstructions

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage

Automated Data Collection

Automated data collection with Serial EM SerialEM
Older notes on Serial EM SerialEmNotes
Serial EM Macros SerialEMMacros
Notes on Shutter Box settings on Tecnai on Low Dose and Serial EM ShutterBox
Serial EM - notes on montages and use of the Navigator MontageNavigator
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList

Film Related

Film Screening And Scanning Overview FilmScreeningAndScanning
Scanning - PDS Densitometer PdsDensitometer
Scanning - Zeiss Densitometer ZeissDensitometer
Screening films with Optical Bench OpticalBench

Lab Protocols

Main protocols page CemProtoc

Grid Preparation

Grid prep - general information CemProtocGrids
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
Plastic Coated Grid PlasticCoatedGrid
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Considerations for electron tomography sample preperation CemProtocET
Fiducial Markers for Tomography PPFiducialsTomography
Carbon Coating instructions CarbonCoating
Carbon Coating using Thread CarbonThread
Carbon Coating using Carbon Rod CarbonRod
Metal Shadowing MetalShadowing

Staining

Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining

Cryo

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
High pressure freezing CemProtocHPFU
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc

Image Processing

Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
EmIP - How to Plot 1D CTF profile of an image FileConversion
Helical Processing : Initial steps HelicalProcessing
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
Helical Reconstruction with EmIP HelicalReconstruction
Processing - electron crystallography CemProtocProcessEC
Processing - tomographic data CemProtocProcessET
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Processing - Single particle analysis CemProtocProcessSPA
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub


General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. All mirrored sites can be found on: CemTwikiToWebListTest. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact the CEM staff.

  • Set ALLOWTOPICVIEW =

-- EdEng - 17 May 2012

Added:
>
>

Revision 1518 May 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Contents
Changed:
<
<
---+Overview  
>
>
Overview  
 
Interested in Cryoem? (How to begin a project) CemInterested
Cryoem at NYSBC CemIntroduction
General info on cryoem at NYSBC CemGeneralInfo
Cryoem Operations committee CemOpCom
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
How to sign up for CEM equipment at NYSBC CemSignupOverview
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
Publications related to CEM at NYSBC CemPublications
The site map you are now viewing CemSiteMap
Changed:
<
<
---+Equipment  
>
>
Equipment  
 
Equipment overview - Sample preparation CemSamplePrep
Changed:
<
<
---++Plasma cleaners  
>
>
Plasma cleaners  
 
Plasma cleaners CemPlasmaCleaning
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
Glow Discharge Using Edwards Evaporator GlowDischarge
Changed:
<
<

Cryo

>
>
Cryo  
 
Plunge freezing equipment CemPlungeFreezer
High Pressure Freezing Menu HighPressFreezer
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
Use of the Oscilloscope/ Matlab MatlabOscilloscope
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Main page for all Microscopes CryoEM
Microscope overview page CemMicroscopes
CEM Parameters CemParameters
How to Find The Beam FindBeam
Microscope Shut Down ShutDown

Jeol 1230

Jeol 1230 description Jeol1230Description
Jeol 1230 Information Jeol1230Information
Jeol 1230 Instructions Jeol1230Instructions
Jeo l1230 filament exchange instructions FilamentExchange

Jeol 2100

Jeol 2100 description Jeol2100Description
Jeol 2100 Information Jeol2100Information
Jeol 2100 Basic Instructions Jeol2100Basicinstructions
Jeol 2100 Instructions Jeol2100Instructions

Jeol 3200

Jeol 3200 description Jeol3200Description
Jeol 3200Information Jeol3200Information
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
Tecnai Information TecnaiInformation
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
Tecnai Instructions TecnaiInstructions
Tecnai advanced instructions TecnaiAdvanced
Ccd Blank Enable, specific for Tecnai F20 CcdBlankEnable
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

FEI Helios Dual Beam overview HeliosDescription
Helios Instructions CemHeliosInstructions

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage

Automated Data Collection

Automated data collection with Serial EM SerialEM
Older notes on Serial EM SerialEmNotes
Serial EM Macros SerialEMMacros
Notes on Shutter Box settings on Tecnai on Low Dose and Serial EM ShutterBox
Serial EM - notes on montages and use of the Navigator MontageNavigator
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList

Film Related

Film Screening And Scanning Overview FilmScreeningAndScanning
Scanning - PDS Densitometer PdsDensitometer
Scanning - Zeiss Densitometer ZeissDensitometer
Screening films with Optical Bench OpticalBench

Lab Protocols

Main protocols page CemProtoc

Grid Preparation

Grid prep - general information CemProtocGrids
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
Plastic Coated Grid PlasticCoatedGrid
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Considerations for electron tomography sample preperation CemProtocET
Fiducial Markers for Tomography PPFiducialsTomography
Carbon Coating instructions CarbonCoating
Carbon Coating using Thread CarbonThread
Carbon Coating using Carbon Rod CarbonRod
Metal Shadowing MetalShadowing

Staining

Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining

Cryo

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
High pressure freezing CemProtocHPFU
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc

Image Processing

Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
EmIP - How to Plot 1D CTF profile of an image FileConversion
Helical Processing : Initial steps HelicalProcessing
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
Helical Reconstruction with EmIP HelicalReconstruction
Processing - electron crystallography CemProtocProcessEC
Processing - tomographic data CemProtocProcessET
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Processing - Single particle analysis CemProtocProcessSPA
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub


General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. All mirrored sites can be found on: CemTwikiToWebListTest. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact the CEM staff.

  • Set ALLOWTOPICVIEW =

-- EdEng - 17 May 2012

Revision 1418 May 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Contents
Changed:
<
<

Overview

>
>
---+Overview  
 
Interested in Cryoem? (How to begin a project) CemInterested
Cryoem at NYSBC CemIntroduction
General info on cryoem at NYSBC CemGeneralInfo
Cryoem Operations committee CemOpCom
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
How to sign up for CEM equipment at NYSBC CemSignupOverview
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
Publications related to CEM at NYSBC CemPublications
The site map you are now viewing CemSiteMap
Changed:
<
<
>
>
---+Equipment  
Deleted:
<
<

Equipment

 
Equipment overview - Sample preparation CemSamplePrep
Changed:
<
<
>
>
---++Plasma cleaners  
Deleted:
<
<

Plasma cleaners

 
Plasma cleaners CemPlasmaCleaning
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
Glow Discharge Using Edwards Evaporator GlowDischarge

Cryo

Plunge freezing equipment CemPlungeFreezer
High Pressure Freezing Menu HighPressFreezer
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
Use of the Oscilloscope/ Matlab MatlabOscilloscope
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Main page for all Microscopes CryoEM
Microscope overview page CemMicroscopes
CEM Parameters CemParameters
How to Find The Beam FindBeam
Microscope Shut Down ShutDown

Jeol 1230

Jeol 1230 description Jeol1230Description
Jeol 1230 Information Jeol1230Information
Jeol 1230 Instructions Jeol1230Instructions
Jeo l1230 filament exchange instructions FilamentExchange

Jeol 2100

Jeol 2100 description Jeol2100Description
Jeol 2100 Information Jeol2100Information
Jeol 2100 Basic Instructions Jeol2100Basicinstructions
Jeol 2100 Instructions Jeol2100Instructions

Jeol 3200

Jeol 3200 description Jeol3200Description
Jeol 3200Information Jeol3200Information
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
Tecnai Information TecnaiInformation
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
Tecnai Instructions TecnaiInstructions
Tecnai advanced instructions TecnaiAdvanced
Ccd Blank Enable, specific for Tecnai F20 CcdBlankEnable
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

FEI Helios Dual Beam overview HeliosDescription
Helios Instructions CemHeliosInstructions

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage

Automated Data Collection

Automated data collection with Serial EM SerialEM
Older notes on Serial EM SerialEmNotes
Serial EM Macros SerialEMMacros
Notes on Shutter Box settings on Tecnai on Low Dose and Serial EM ShutterBox
Serial EM - notes on montages and use of the Navigator MontageNavigator
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList

Film Related

Film Screening And Scanning Overview FilmScreeningAndScanning
Scanning - PDS Densitometer PdsDensitometer
Scanning - Zeiss Densitometer ZeissDensitometer
Screening films with Optical Bench OpticalBench

Lab Protocols

Main protocols page CemProtoc

Grid Preparation

Grid prep - general information CemProtocGrids
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
Plastic Coated Grid PlasticCoatedGrid
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Considerations for electron tomography sample preperation CemProtocET
Fiducial Markers for Tomography PPFiducialsTomography
Carbon Coating instructions CarbonCoating
Carbon Coating using Thread CarbonThread
Carbon Coating using Carbon Rod CarbonRod
Metal Shadowing MetalShadowing

Staining

Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining

Cryo

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
High pressure freezing CemProtocHPFU
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc

Image Processing

Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
EmIP - How to Plot 1D CTF profile of an image FileConversion
Helical Processing : Initial steps HelicalProcessing
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
Helical Reconstruction with EmIP HelicalReconstruction
Processing - electron crystallography CemProtocProcessEC
Processing - tomographic data CemProtocProcessET
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Processing - Single particle analysis CemProtocProcessSPA
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub


General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. All mirrored sites can be found on: CemTwikiToWebListTest. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact the CEM staff.

  • Set ALLOWTOPICVIEW =

-- EdEng - 17 May 2012

Revision 1318 May 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Contents

Overview

Interested in Cryoem? (How to begin a project) CemInterested
Cryoem at NYSBC CemIntroduction
General info on cryoem at NYSBC CemGeneralInfo
Cryoem Operations committee CemOpCom
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
How to sign up for CEM equipment at NYSBC CemSignupOverview
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
Publications related to CEM at NYSBC CemPublications
The site map you are now viewing CemSiteMap

Equipment

Equipment overview - Sample preparation CemSamplePrep

Plasma cleaners

Plasma cleaners CemPlasmaCleaning
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
Glow Discharge Using Edwards Evaporator GlowDischarge

Cryo

Plunge freezing equipment CemPlungeFreezer
High Pressure Freezing Menu HighPressFreezer
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
Use of the Oscilloscope/ Matlab MatlabOscilloscope
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Main page for all Microscopes CryoEM
Added:
>
>
Microscope overview page CemMicroscopes
 
CEM Parameters CemParameters
How to Find The Beam FindBeam
Microscope Shut Down ShutDown

Jeol 1230

Jeol 1230 description Jeol1230Description
Jeol 1230 Information Jeol1230Information
Jeol 1230 Instructions Jeol1230Instructions
Jeo l1230 filament exchange instructions FilamentExchange

Jeol 2100

Jeol 2100 description Jeol2100Description
Jeol 2100 Information Jeol2100Information
Jeol 2100 Basic Instructions Jeol2100Basicinstructions
Jeol 2100 Instructions Jeol2100Instructions

Jeol 3200

Jeol 3200 description Jeol3200Description
Jeol 3200Information Jeol3200Information
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
Tecnai Information TecnaiInformation
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
Tecnai Instructions TecnaiInstructions
Tecnai advanced instructions TecnaiAdvanced
Ccd Blank Enable, specific for Tecnai F20 CcdBlankEnable
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

FEI Helios Dual Beam overview HeliosDescription
Helios Instructions CemHeliosInstructions

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage

Automated Data Collection

Automated data collection with Serial EM SerialEM
Older notes on Serial EM SerialEmNotes
Serial EM Macros SerialEMMacros
Notes on Shutter Box settings on Tecnai on Low Dose and Serial EM ShutterBox
Serial EM - notes on montages and use of the Navigator MontageNavigator
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList

Film Related

Film Screening And Scanning Overview FilmScreeningAndScanning
Scanning - PDS Densitometer PdsDensitometer
Scanning - Zeiss Densitometer ZeissDensitometer
Screening films with Optical Bench OpticalBench

Lab Protocols

Main protocols page CemProtoc

Grid Preparation

Grid prep - general information CemProtocGrids
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
Plastic Coated Grid PlasticCoatedGrid
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Considerations for electron tomography sample preperation CemProtocET
Fiducial Markers for Tomography PPFiducialsTomography
Carbon Coating instructions CarbonCoating
Carbon Coating using Thread CarbonThread
Carbon Coating using Carbon Rod CarbonRod
Metal Shadowing MetalShadowing

Staining

Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining

Cryo

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
High pressure freezing CemProtocHPFU
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc

Image Processing

Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
EmIP - How to Plot 1D CTF profile of an image FileConversion
Helical Processing : Initial steps HelicalProcessing
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
Helical Reconstruction with EmIP HelicalReconstruction
Processing - electron crystallography CemProtocProcessEC
Processing - tomographic data CemProtocProcessET
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Processing - Single particle analysis CemProtocProcessSPA
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub


General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. All mirrored sites can be found on: CemTwikiToWebListTest. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact the CEM staff.

  • Set ALLOWTOPICVIEW =

-- EdEng - 17 May 2012

Revision 1217 May 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Contents

Overview

Interested in Cryoem? (How to begin a project) CemInterested
Cryoem at NYSBC CemIntroduction
General info on cryoem at NYSBC CemGeneralInfo
Cryoem Operations committee CemOpCom
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
How to sign up for CEM equipment at NYSBC CemSignupOverview
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
Publications related to CEM at NYSBC CemPublications
The site map you are now viewing CemSiteMap

Equipment

Equipment overview - Sample preparation CemSamplePrep

Plasma cleaners

Plasma cleaners CemPlasmaCleaning
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
Glow Discharge Using Edwards Evaporator GlowDischarge

Cryo

Plunge freezing equipment CemPlungeFreezer
High Pressure Freezing Menu HighPressFreezer
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
Use of the Oscilloscope/ Matlab MatlabOscilloscope
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Main page for all Microscopes CryoEM
CEM Parameters CemParameters
How to Find The Beam FindBeam
Microscope Shut Down ShutDown

Jeol 1230

Jeol 1230 description Jeol1230Description
Jeol 1230 Information Jeol1230Information
Jeol 1230 Instructions Jeol1230Instructions
Jeo l1230 filament exchange instructions FilamentExchange

Jeol 2100

Jeol 2100 description Jeol2100Description
Jeol 2100 Information Jeol2100Information
Jeol 2100 Basic Instructions Jeol2100Basicinstructions
Jeol 2100 Instructions Jeol2100Instructions

Jeol 3200

Jeol 3200 description Jeol3200Description
Jeol 3200Information Jeol3200Information
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
Tecnai Information TecnaiInformation
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
Tecnai Instructions TecnaiInstructions
Tecnai advanced instructions TecnaiAdvanced
Ccd Blank Enable, specific for Tecnai F20 CcdBlankEnable
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

FEI Helios Dual Beam overview HeliosDescription
Helios Instructions CemHeliosInstructions

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage

Automated Data Collection

Automated data collection with Serial EM SerialEM
Older notes on Serial EM SerialEmNotes
Serial EM Macros SerialEMMacros
Notes on Shutter Box settings on Tecnai on Low Dose and Serial EM ShutterBox
Serial EM - notes on montages and use of the Navigator MontageNavigator
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList

Film Related

Film Screening And Scanning Overview FilmScreeningAndScanning
Scanning - PDS Densitometer PdsDensitometer
Scanning - Zeiss Densitometer ZeissDensitometer
Screening films with Optical Bench OpticalBench

Lab Protocols

Main protocols page CemProtoc

Grid Preparation

Grid prep - general information CemProtocGrids
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
Plastic Coated Grid PlasticCoatedGrid
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Considerations for electron tomography sample preperation CemProtocET
Fiducial Markers for Tomography PPFiducialsTomography
Carbon Coating instructions CarbonCoating
Carbon Coating using Thread CarbonThread
Carbon Coating using Carbon Rod CarbonRod
Metal Shadowing MetalShadowing

Staining

Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining

Cryo

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
High pressure freezing CemProtocHPFU
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc

Image Processing

Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
EmIP - How to Plot 1D CTF profile of an image FileConversion
Helical Processing : Initial steps HelicalProcessing
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
Helical Reconstruction with EmIP HelicalReconstruction
Processing - electron crystallography CemProtocProcessEC
Processing - tomographic data CemProtocProcessET
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Processing - Single particle analysis CemProtocProcessSPA
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub


General info about this sitemap

Changed:
<
<
This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact the CEM staff.
>
>
This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. All mirrored sites can be found on: CemTwikiToWebListTest. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact the CEM staff.
 

  • Set ALLOWTOPICVIEW =

-- EdEng - 17 May 2012

Deleted:
<
<

Revision 1117 May 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Contents

Overview

Interested in Cryoem? (How to begin a project) CemInterested
Cryoem at NYSBC CemIntroduction
General info on cryoem at NYSBC CemGeneralInfo
Cryoem Operations committee CemOpCom
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
How to sign up for CEM equipment at NYSBC CemSignupOverview
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
Publications related to CEM at NYSBC CemPublications
The site map you are now viewing CemSiteMap

Equipment

Equipment overview - Sample preparation CemSamplePrep

Plasma cleaners

Plasma cleaners CemPlasmaCleaning
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
Changed:
<
<
GlowDischarge Using Edwards Evaporator GlowDischarge
>
>
Glow Discharge Using Edwards Evaporator GlowDischarge
 

Cryo

Plunge freezing equipment CemPlungeFreezer
High Pressure Freezing Menu HighPressFreezer
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
Use of the Oscilloscope/ Matlab MatlabOscilloscope
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Main page for all Microscopes CryoEM
Changed:
<
<
CemParameters CemParameters
>
>
CEM Parameters CemParameters
 
How to Find The Beam FindBeam
Microscope Shut Down ShutDown

Jeol 1230

Jeol 1230 description Jeol1230Description
Changed:
<
<
Jeol2100Information Jeol1230Information
Jeol1230Instructions Jeol1230Instructions
Jeol1230 filament exchange instructions FilamentExchange
>
>
Jeol 1230 Information Jeol1230Information
Jeol 1230 Instructions Jeol1230Instructions
Jeo l1230 filament exchange instructions FilamentExchange
 

Jeol 2100

Jeol 2100 description Jeol2100Description
Changed:
<
<
Jeol2100 Information Jeol2100Information
Jeol2100 Basic Instructions Jeol2100Basicinstructions
Jeol2100 Instructions Jeol2100Instructions
>
>
Jeol 2100 Information Jeol2100Information
Jeol 2100 Basic Instructions Jeol2100Basicinstructions
Jeol 2100 Instructions Jeol2100Instructions
 

Jeol 3200

Jeol 3200 description Jeol3200Description
Jeol 3200Information Jeol3200Information
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
Changed:
<
<
TecnaiInformation TecnaiInformation
>
>
Tecnai Information TecnaiInformation
 
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
Changed:
<
<
TecnaiInstructions TecnaiInstructions
>
>
Tecnai Instructions TecnaiInstructions
 
Tecnai advanced instructions TecnaiAdvanced
Changed:
<
<
CcdBlankEnable, specific for Tecnai F20 CcdBlankEnable
>
>
Ccd Blank Enable, specific for Tecnai F20 CcdBlankEnable
 
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

Changed:
<
<
DualBeam overview HeliosDescription
>
>
FEI Helios Dual Beam overview HeliosDescription
Added:
>
>
Helios Instructions CemHeliosInstructions
 

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage

Automated Data Collection

Changed:
<
<
Automated data collection with SerialEM SerialEM
Older notes on SerialEM SerialEmNotes
>
>
Automated data collection with Serial EM SerialEM
Older notes on Serial EM SerialEmNotes
 
Serial EM Macros SerialEMMacros
Changed:
<
<
Notes on Shutter Box settings on Tecnai on Low Dose and SerialEM ShutterBox
SerialEM - notes on montages and use of the Navigator MontageNavigator
>
>
Notes on Shutter Box settings on Tecnai on Low Dose and Serial EM ShutterBox
Serial EM - notes on montages and use of the Navigator MontageNavigator
 
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList

Film Related

Film Screening And Scanning Overview FilmScreeningAndScanning
Scanning - PDS Densitometer PdsDensitometer
Scanning - Zeiss Densitometer ZeissDensitometer
Screening films with Optical Bench OpticalBench

Lab Protocols

Main protocols page CemProtoc

Grid Preparation

Grid prep - general information CemProtocGrids
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
Changed:
<
<
PlasticCoatedGrid PlasticCoatedGrid
>
>
Plastic Coated Grid PlasticCoatedGrid
 
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Considerations for electron tomography sample preperation CemProtocET
Fiducial Markers for Tomography PPFiducialsTomography
Carbon Coating instructions CarbonCoating
Carbon Coating using Thread CarbonThread
Carbon Coating using Carbon Rod CarbonRod
Metal Shadowing MetalShadowing

Staining

Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining

Cryo

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
High pressure freezing CemProtocHPFU
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc

Image Processing

Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
Changed:
<
<
EmIPHow? to Plot 1D CTF profile of an image FileConversion
>
>
EmIP - How to Plot 1D CTF profile of an image FileConversion
 
Helical Processing : Initial steps HelicalProcessing
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
Helical Reconstruction with EmIP HelicalReconstruction
Processing - electron crystallography CemProtocProcessEC
Processing - tomographic data CemProtocProcessET
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Processing - Single particle analysis CemProtocProcessSPA
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub


General info about this sitemap

Changed:
<
<
This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact BillRice or EdEng.
>
>
This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact the CEM staff.
 

  • Set ALLOWTOPICVIEW =

-- EdEng - 17 May 2012

Added:
>
>

Revision 1017 May 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Contents

Overview

Interested in Cryoem? (How to begin a project) CemInterested
Cryoem at NYSBC CemIntroduction
General info on cryoem at NYSBC CemGeneralInfo
Cryoem Operations committee CemOpCom
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
How to sign up for CEM equipment at NYSBC CemSignupOverview
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
Publications related to CEM at NYSBC CemPublications
The site map you are now viewing CemSiteMap

Equipment

Equipment overview - Sample preparation CemSamplePrep

Plasma cleaners

Plasma cleaners CemPlasmaCleaning
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
GlowDischarge Using Edwards Evaporator GlowDischarge

Cryo

Plunge freezing equipment CemPlungeFreezer
High Pressure Freezing Menu HighPressFreezer
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
Use of the Oscilloscope/ Matlab MatlabOscilloscope
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Changed:
<
<
Main page for all Microscopes
>
>
Main page for all Microscopes CryoEM
Deleted:
<
<
Another page for all microscopes twiki
 
CemParameters CemParameters
How to Find The Beam FindBeam
Microscope Shut Down ShutDown

Jeol 1230

Jeol 1230 description Jeol1230Description
Jeol2100Information Jeol1230Information
Jeol1230Instructions Jeol1230Instructions
Jeol1230 filament exchange instructions FilamentExchange

Jeol 2100

Jeol 2100 description Jeol2100Description
Jeol2100 Information Jeol2100Information
Jeol2100 Basic Instructions Jeol2100Basicinstructions
Jeol2100 Instructions Jeol2100Instructions

Jeol 3200

Jeol 3200 description Jeol3200Description
Jeol 3200Information Jeol3200Information
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
TecnaiInformation TecnaiInformation
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
TecnaiInstructions TecnaiInstructions
Tecnai advanced instructions TecnaiAdvanced
CcdBlankEnable, specific for Tecnai F20 CcdBlankEnable
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

DualBeam overview HeliosDescription

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage

Automated Data Collection

Changed:
<
<
Automated data collection with SerialEM   SerialEM
>
>
Automated data collection with SerialEM SerialEM
 
Older notes on SerialEM SerialEmNotes
Serial EM Macros SerialEMMacros
Notes on Shutter Box settings on Tecnai on Low Dose and SerialEM ShutterBox
SerialEM - notes on montages and use of the Navigator MontageNavigator
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList

Film Related

Film Screening And Scanning Overview FilmScreeningAndScanning
Scanning - PDS Densitometer PdsDensitometer
Scanning - Zeiss Densitometer ZeissDensitometer
Screening films with Optical Bench OpticalBench

Lab Protocols

Main protocols page CemProtoc

Grid Preparation

Grid prep - general information CemProtocGrids
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
PlasticCoatedGrid PlasticCoatedGrid
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Considerations for electron tomography sample preperation CemProtocET
Fiducial Markers for Tomography PPFiducialsTomography
Carbon Coating instructions CarbonCoating
Carbon Coating using Thread CarbonThread
Carbon Coating using Carbon Rod CarbonRod
Metal Shadowing MetalShadowing

Staining

Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining

Cryo

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
High pressure freezing CemProtocHPFU
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc

Image Processing

Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
EmIPHow? to Plot 1D CTF profile of an image FileConversion
Helical Processing : Initial steps HelicalProcessing
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
Helical Reconstruction with EmIP HelicalReconstruction
Processing - electron crystallography CemProtocProcessEC
Processing - tomographic data CemProtocProcessET
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Processing - Single particle analysis CemProtocProcessSPA
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub
Changed:
<
<
>
>

Added:
>
>

 

General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact BillRice or EdEng.

  • Set ALLOWTOPICVIEW =

-- EdEng - 17 May 2012

Revision 917 May 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Contents
Changed:
<
<

Overview

>
>

Overview

 
Interested in Cryoem? (How to begin a project) CemInterested
Changed:
<
<
Cryoem at NYSBC General info on cryoem at NYSBC Cryoem Operations committee twiki
>
>
Cryoem at NYSBC CemIntroduction
General info on cryoem at NYSBC CemGeneralInfo
Cryoem Operations committee CemOpCom
 
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
Deleted:
<
<
Main cryoem page Publications related to CEM at NYSBC
 
How to sign up for CEM equipment at NYSBC CemSignupOverview
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
Added:
>
>
Publications related to CEM at NYSBC CemPublications
 
The site map you are now viewing CemSiteMap
Changed:
<
<

Equipment

>
>

Equipment

 
Equipment overview - Sample preparation CemSamplePrep
Added:
>
>

Plasma cleaners

 
Plasma cleaners CemPlasmaCleaning
Deleted:
<
<
Plunge freezing equipment CemPlungeFreezer
 
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
GlowDischarge Using Edwards Evaporator GlowDischarge
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<
<

Cryo

>
>

Cryo

Added:
>
>
Plunge freezing equipment CemPlungeFreezer
 
High Pressure Freezing Menu HighPressFreezer
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
Use of the Oscilloscope/ Matlab MatlabOscilloscope
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Main page for all Microscopes Another page for all microscopes twiki
CemParameters CemParameters
How to Find The Beam FindBeam
Microscope Shut Down ShutDown

Jeol 1230

Jeol 1230 description Jeol1230Description
Jeol2100Information Jeol1230Information
Jeol1230Instructions Jeol1230Instructions
Jeol1230 filament exchange instructions FilamentExchange

Jeol 2100

Jeol 2100 description Jeol2100Description
Jeol2100 Information Jeol2100Information
Jeol2100 Basic Instructions Jeol2100Basicinstructions
Jeol2100 Instructions Jeol2100Instructions

Jeol 3200

Jeol 3200 description Jeol3200Description
Jeol 3200Information Jeol3200Information
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
TecnaiInformation TecnaiInformation
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
TecnaiInstructions TecnaiInstructions
Tecnai advanced instructions TecnaiAdvanced
CcdBlankEnable, specific for Tecnai F20 CcdBlankEnable
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

DualBeam overview HeliosDescription

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage

Automated Data Collection

Automated data collection with SerialEM   SerialEM
Older notes on SerialEM SerialEmNotes
Serial EM Macros SerialEMMacros
Changed:
<
<
Notes on Shutter Box settings on Tecnai on Low Dose and SerialEM twiki SerialEM - notes on montages and use of the Navigator twiki
>
>
Notes on Shutter Box settings on Tecnai on Low Dose and SerialEM ShutterBox
SerialEM - notes on montages and use of the Navigator MontageNavigator
 
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList
Deleted:
<
<
Film Related Film Screening And Scanning Overview twiki Scanning - PDS Densitometer twiki Scanning - Zeiss Densitometer twiki Screening films with Optical Bench twiki Courses Graduate level course in cryo-EM Other seminars and courses in Cryo-EM twiki Previous EM Journal Clubs twiki
 
Changed:
<
<

Lab Protocols

>
>

Film Related

Added:
>
>
Film Screening And Scanning Overview FilmScreeningAndScanning
Scanning - PDS Densitometer PdsDensitometer
Scanning - Zeiss Densitometer ZeissDensitometer
Screening films with Optical Bench OpticalBench

Lab Protocols

 
Main protocols page CemProtoc
Changed:
<
<

Grid Preparation

>
>

Grid Preparation

 
Grid prep - general information CemProtocGrids
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
PlasticCoatedGrid PlasticCoatedGrid
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Considerations for electron tomography sample preperation CemProtocET
Fiducial Markers for Tomography PPFiducialsTomography
Added:
>
>
Carbon Coating instructions CarbonCoating
Carbon Coating using Thread CarbonThread
Carbon Coating using Carbon Rod CarbonRod
Metal Shadowing MetalShadowing
 
Changed:
<
<

Staining

>
>

Staining

 
Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining
Changed:
<
<

Plunge Freezing

>
>

Cryo

 
Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
Deleted:
<
<
a129 1
 
High pressure freezing CemProtocHPFU
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc

Image Processing

Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
EmIPHow? to Plot 1D CTF profile of an image FileConversion
Helical Processing : Initial steps HelicalProcessing
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
Helical Reconstruction with EmIP HelicalReconstruction
Processing - electron crystallography CemProtocProcessEC
Processing - tomographic data CemProtocProcessET
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Processing - Single particle analysis CemProtocProcessSPA
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub

General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact BillRice or EdEng.

  • Set ALLOWTOPICVIEW =

-- EdEng - 17 May 2012

Revision 817 May 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Contents

Overview

Changed:
<
<
Interested in Cryoem?
>
>
Interested in Cryoem? (How to begin a project) CemInterested
 Cryoem at NYSBC General info on cryoem at NYSBC Cryoem Operations committee twiki
Changed:
<
<
EM as a technique in structural biology EM as a technique in structural biology (from twiki)
>
>
EM (TEM) as a technique in structural biology CemProtocStructbiolTEM
Overview of Electron Crystallography CemProtocEC
 Main cryoem page Publications related to CEM at NYSBC
Changed:
<
<
How to sign up for CEM equipment at NYSBC twiki
>
>
How to sign up for CEM equipment at NYSBC CemSignupOverview
 
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
The site map you are now viewing CemSiteMap

Equipment

Changed:
<
<
Equipment -- sample prep Equipment -- main plasma cleaner for glow discharge Plunge freezing equipment GlowDischarge Using Edwards Evaporator twiki Edwards Vacuum Evaporator overview twiki HpfSupplies twiki
>
>
Equipment overview - Sample preparation CemSamplePrep
Plasma cleaners CemPlasmaCleaning
Plunge freezing equipment CemPlungeFreezer
Edwards Vacuum Evaporator overview VacuumEvaporator
Edwards maintenance MaintenanceNotes
GlowDischarge Using Edwards Evaporator GlowDischarge

Cryo

 
High Pressure Freezing Menu HighPressFreezer
Added:
>
>
Hpf Supplies HpfSupplies
Using the Bal-Tec High Pressure Freezer HpfUse
Using the Wohlwend High Pressure Freezer WohlwendUse
 
Use of the Oscilloscope/ Matlab MatlabOscilloscope
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<
<
HpfUse twiki WohlwendUse twiki
>
>
Pressure Regulator PressureRegulator
Oscilloscope Recorder OscilloscopeRecorder
Deleted:
<
<
PressureRegulator twiki
 
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion

Microscopes

Main page for all Microscopes Another page for all microscopes twiki
Changed:
<
<
CemParameters twiki jeol 1230 description Jeol1230Instructions twiki
>
>
CemParameters CemParameters
How to Find The Beam FindBeam
Microscope Shut Down ShutDown
Deleted:
<
<
Jeol1230Information twiki Jeol1230 filament exchange instructions twiki jeol 2100 description Jeol2100Information twiki Jeol2100Basicinstructions twiki Jeol2100Instructions twiki jeol 3200 description Jeol3200Information twiki Jeol3200Basicinstructions twiki Jeol3200Instructions twiki How to collect dual tilt tomograms on Jeol3200 twiki Tecnai F20 description TecnaiInformation twiki TecnaiInstructions twiki Tecnai advanced instructions twiki F20 daily checklist twiki CcdBlankEnable, specific for Tecnai F20 twiki Microscope Shut Down twiki How to Find The Beam twiki How to Insert a Room Temperature Sample twiki How to Insert a CryoSample? twiki General Instructions for using cryo-holders twiki How to take a CCD image with Tietz software twiki How to take a film image twiki
 
Added:
>
>

Jeol 1230

Jeol 1230 description Jeol1230Description
Jeol2100Information Jeol1230Information
Jeol1230Instructions Jeol1230Instructions
Jeol1230 filament exchange instructions FilamentExchange

Jeol 2100

Jeol 2100 description Jeol2100Description
Jeol2100 Information Jeol2100Information
Jeol2100 Basic Instructions Jeol2100Basicinstructions
Jeol2100 Instructions Jeol2100Instructions

Jeol 3200

Jeol 3200 description Jeol3200Description
Jeol 3200Information Jeol3200Information
Jeol 3200 Basicinstructions Jeol3200Basicinstructions
Jeol 3200 Instructions Jeol3200Instructions
How to collect dual tilt tomograms on Jeol3200 DualTilt

Tecnai F20

Tecnai F20 description TecnaiDescription
TecnaiInformation TecnaiInformation
New user setup and brief interface introduction Newf20User
F20 daily checklist F20Checklist
TecnaiInstructions TecnaiInstructions
Tecnai advanced instructions TecnaiAdvanced
CcdBlankEnable, specific for Tecnai F20 CcdBlankEnable
How to Insert a Room Temperature Sample InsertRoomTemperatureSample
How to Insert a CryoSample? InsertCryoSample

Helios

DualBeam overview HeliosDescription

Data Collection

Cryo Electron Microscopy Information and Instructions CryoEM
General Instructions for using cryo-holders ColdStage
How to take a CCD image with Tietz software CcdImage
How to take a film image FilmImage
 

Automated Data Collection

Changed:
<
<
Automated data collection with SerialEM twiki Older notes on SerialEM twiki
>
>
Automated data collection with SerialEM   SerialEM
Older notes on SerialEM SerialEmNotes
Added:
>
>
Serial EM Macros SerialEMMacros
 Notes on Shutter Box settings on Tecnai on Low Dose and SerialEM twiki SerialEM - notes on montages and use of the Navigator twiki
Changed:
<
<
Notes on Cem Robotics using JEOL1230 twiki Checklist before using 1230 Robot twiki
>
>
Notes on Cem Robotics using JEOL1230 CemRobotics
Checklist before using 1230 Robot 1230CheckList
 Film Related Film Screening And Scanning Overview twiki Scanning - PDS Densitometer twiki Scanning - Zeiss Densitometer twiki Screening films with Optical Bench twiki Courses Graduate level course in cryo-EM Other seminars and courses in Cryo-EM twiki Previous EM Journal Clubs twiki

Lab Protocols

Changed:
<
<
Main protocols page twiki
>
>
Main protocols page CemProtoc
Deleted:
<
<

Plunge Freezing

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
 

Grid Preparation

Added:
>
>
Grid prep - general information CemProtocGrids
 
Solid carbon films PPSolidCarbonFilms
Pioloform Grids PPPioloformGrids
Added:
>
>
PlasticCoatedGrid PlasticCoatedGrid
 
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Added:
>
>
Considerations for electron tomography sample preperation CemProtocET
 
Fiducial Markers for Tomography PPFiducialsTomography
Deleted:
<
<
Grid prep - general information twiki
 
Changed:
<
<
high pressure freezing twiki
>
>

Staining

Added:
>
>
Staining CemProtocStaining
Negative staining PPNegativeStaining
Positive staining PPPositiveStaining

Plunge Freezing

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing
a129 1
High pressure freezing CemProtocHPFU
 
Notes on cryo sectioning Chyongere
Freeze Substitution Principles FreezeSubstitution
Freeze Substitution Protocol FreezeSubProtoc
Deleted:
<
<
Staining twiki Negative staining twiki Positive staining twiki PlasticCoatedGrid twiki
 

Image Processing

Changed:
<
<
Carbon Coating using Thread twiki Carbon Coating using Carbon Rod twiki Metal Shadowing twiki
>
>
Image processing menu ImageProcessing
Overview of Cluster CemCluster
List of supported software SoftWare
 
Overview of software in use CemProtocProcessoverview
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
EmIPHow? to Plot 1D CTF profile of an image FileConversion
Helical Processing : Initial steps HelicalProcessing
Changed:
<
<

Image Processing and computing

>
>
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab CemHelicalPrograms
 
Helical Reconstruction with EmIP HelicalReconstruction
Changed:
<
<
Overview of software in use twiki
>
>
Processing - electron crystallography CemProtocProcessEC
 
Processing - tomographic data CemProtocProcessET
Changed:
<
<
Description of EMIP, a GUI for various image processing techniques twiki Processing - electron crystallography twiki Processing - tomographic data twiki
>
>
Instructions for processing tomograms with the Protomo package FsuTomograms
Instructions for calculating a random conical tilt reconstruction CemRandomConicalTilt
Principles of single particle analysis CemProtocSPA
Added:
>
>
Processing - Single particle analysis CemProtocProcessSPA
 
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Changed:
<
<
Processing - Helical Reconstruction twiki Processing - Single particle analysis twiki Background - single particle analysis Background - single particle analysis (from twiki) Electron Crystallography twiki
>
>
Conversion of a set of Digital Micrograph files to Tiff format DigitalMicrograph2TIF
IMOD - conversion of MRC stack to series of tif images ImodNotes

CEM IT resources

CEM IT CemIT
Deleted:
<
<
Electron tomography protocols twiki
 
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub

General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact BillRice or EdEng.

Added:
>
>
  • Set ALLOWTOPICVIEW =
 -- EdEng - 17 May 2012

Revision 717 May 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Contents

Overview

Interested in Cryoem? Cryoem at NYSBC General info on cryoem at NYSBC Cryoem Operations committee twiki EM as a technique in structural biology EM as a technique in structural biology (from twiki) Main cryoem page Publications related to CEM at NYSBC How to sign up for CEM equipment at NYSBC twiki
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
The site map you are now viewing CemSiteMap

Equipment

Equipment -- sample prep Equipment -- main plasma cleaner for glow discharge Plunge freezing equipment GlowDischarge Using Edwards Evaporator twiki Edwards Vacuum Evaporator overview twiki HpfSupplies twiki
Changed:
<
<
High Pressure Freezer twiki
>
>
High Pressure Freezing Menu HighPressFreezer
Added:
>
>
Use of the Oscilloscope/ Matlab MatlabOscilloscope
 HpfUse twiki WohlwendUse twiki PressureRegulator twiki
Changed:
<
<
Preparation of microtome for cryo-sectioning twiki Use of the Oscilloscope/ Matlab twiki
>
>
Cryo Ultra Microtomy Menu CryoUltraMicrotomy
Preparation of microtome for cryo-sectioning MicrotomeConversion
 

Microscopes

Main page for all Microscopes Another page for all microscopes twiki CemParameters twiki jeol 1230 description Jeol1230Instructions twiki Jeol1230Information twiki Jeol1230 filament exchange instructions twiki jeol 2100 description Jeol2100Information twiki Jeol2100Basicinstructions twiki Jeol2100Instructions twiki jeol 3200 description Jeol3200Information twiki Jeol3200Basicinstructions twiki Jeol3200Instructions twiki How to collect dual tilt tomograms on Jeol3200 twiki Tecnai F20 description TecnaiInformation twiki TecnaiInstructions twiki Tecnai advanced instructions twiki F20 daily checklist twiki CcdBlankEnable, specific for Tecnai F20 twiki Microscope Shut Down twiki How to Find The Beam twiki How to Insert a Room Temperature Sample twiki How to Insert a CryoSample? twiki General Instructions for using cryo-holders twiki How to take a CCD image with Tietz software twiki How to take a film image twiki

Automated Data Collection

Automated data collection with SerialEM twiki Older notes on SerialEM twiki Notes on Shutter Box settings on Tecnai on Low Dose and SerialEM twiki SerialEM - notes on montages and use of the Navigator twiki Notes on Cem Robotics using JEOL1230 twiki Checklist before using 1230 Robot twiki Film Related Film Screening And Scanning Overview twiki Scanning - PDS Densitometer twiki Scanning - Zeiss Densitometer twiki Screening films with Optical Bench twiki Courses Graduate level course in cryo-EM Other seminars and courses in Cryo-EM twiki Previous EM Journal Clubs twiki

Lab Protocols

Main protocols page twiki

Plunge Freezing

Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing

Grid Preparation

Added:
>
>
Solid carbon films PPSolidCarbonFilms
 
Pioloform Grids PPPioloformGrids
Changed:
<
<
Grid prep - homemade holey carbon (Claudio) twiki Grid prep - carbon sandwich twiki Grid prep - adding fiducial markers twiki
>
>
Homemade holey carbon (Claudio) PPClaudioHoleyFilms
Homemade holey carbon (triafol) PPTriafolHoleyFilms
Carbon sandwich PPCarbonSandwich
Added:
>
>
Fiducial Markers for Tomography PPFiducialsTomography
 Grid prep - general information twiki
Changed:
<
<
Grid prep - solid carbon films twiki
>
>
Deleted:
<
<
Grid prep - homemade holey carbon (triafol) twiki
 high pressure freezing twiki
Notes on cryo sectioning Chyongere
Changed:
<
<
Notes on cryo sectioning twiki
>
>
Freeze Substitution Principles FreezeSubstitution
 
Freeze Substitution Protocol FreezeSubProtoc
Changed:
<
<
Plunge freezing Theory(from twiki) twiki
>
>
Deleted:
<
<
Plunge Freezing Practical(from twiki) twiki
 Staining twiki Negative staining twiki Positive staining twiki PlasticCoatedGrid twiki
Changed:
<
<
PioloformGrids? twiki Carbon Coating instructions twiki
>
>

Image Processing

 Carbon Coating using Thread twiki Carbon Coating using Carbon Rod twiki Metal Shadowing twiki
Overview of software in use CemProtocProcessoverview
Changed:
<
<
Freeze Substitution Protocol twiki Freeze Substitution twiki
>
>
Image processing software in use at NYSBC CemITApplications
Description of EMIP, a GUI for various image processing techniques EmIP
Added:
>
>
EmIPHow? to Plot 1D CTF profile of an image FileConversion
 
Helical Processing : Initial steps HelicalProcessing

Image Processing and computing

Helical Reconstruction with EmIP HelicalReconstruction
Overview of software in use twiki
Processing - tomographic data CemProtocProcessET
Description of EMIP, a GUI for various image processing techniques twiki Processing - electron crystallography twiki Processing - tomographic data twiki
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Processing - Helical Reconstruction twiki Processing - Single particle analysis twiki Background - single particle analysis Background - single particle analysis (from twiki) Electron Crystallography twiki Electron tomography protocols twiki
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub

General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact BillRice or EdEng.

-- EdEng - 17 May 2012

Revision 617 May 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Contents

Overview

Interested in Cryoem? Cryoem at NYSBC General info on cryoem at NYSBC Cryoem Operations committee twiki EM as a technique in structural biology EM as a technique in structural biology (from twiki) Main cryoem page Publications related to CEM at NYSBC How to sign up for CEM equipment at NYSBC twiki
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
The site map you are now viewing CemSiteMap

Equipment

Equipment -- sample prep Equipment -- main plasma cleaner for glow discharge Plunge freezing equipment GlowDischarge Using Edwards Evaporator twiki Edwards Vacuum Evaporator overview twiki HpfSupplies twiki High Pressure Freezer twiki HpfUse twiki WohlwendUse twiki PressureRegulator twiki Preparation of microtome for cryo-sectioning twiki Use of the Oscilloscope/ Matlab twiki

Microscopes

Main page for all Microscopes Another page for all microscopes twiki CemParameters twiki jeol 1230 description Jeol1230Instructions twiki Jeol1230Information twiki Jeol1230 filament exchange instructions twiki jeol 2100 description Jeol2100Information twiki Jeol2100Basicinstructions twiki Jeol2100Instructions twiki jeol 3200 description Jeol3200Information twiki Jeol3200Basicinstructions twiki Jeol3200Instructions twiki How to collect dual tilt tomograms on Jeol3200 twiki Tecnai F20 description TecnaiInformation twiki TecnaiInstructions twiki Tecnai advanced instructions twiki F20 daily checklist twiki CcdBlankEnable, specific for Tecnai F20 twiki Microscope Shut Down twiki How to Find The Beam twiki How to Insert a Room Temperature Sample twiki How to Insert a CryoSample? twiki General Instructions for using cryo-holders twiki How to take a CCD image with Tietz software twiki How to take a film image twiki

Automated Data Collection

Automated data collection with SerialEM twiki Older notes on SerialEM twiki Notes on Shutter Box settings on Tecnai on Low Dose and SerialEM twiki SerialEM - notes on montages and use of the Navigator twiki Notes on Cem Robotics using JEOL1230 twiki Checklist before using 1230 Robot twiki Film Related Film Screening And Scanning Overview twiki Scanning - PDS Densitometer twiki Scanning - Zeiss Densitometer twiki Screening films with Optical Bench twiki Courses Graduate level course in cryo-EM Other seminars and courses in Cryo-EM twiki Previous EM Journal Clubs twiki

Lab Protocols

Main protocols page twiki
Changed:
<
<
Plunge freezing protocols
>
>

Plunge Freezing

Added:
>
>
Plunge freezing Theory CemProtocPlungefreezing
Plunge freezing protocol PlungeFreezing

Grid Preparation

Pioloform Grids PPPioloformGrids
 Grid prep - homemade holey carbon (Claudio) twiki Grid prep - carbon sandwich twiki Grid prep - adding fiducial markers twiki Grid prep - general information twiki Grid prep - solid carbon films twiki Grid prep - homemade holey carbon (triafol) twiki high pressure freezing twiki
Notes on cryo sectioning Chyongere
Notes on cryo sectioning twiki
Changed:
<
<
Plunge freezing Theory
>
>
Freeze Substitution Protocol FreezeSubProtoc
 Plunge freezing Theory(from twiki) twiki Plunge Freezing Practical(from twiki) twiki Staining twiki Negative staining twiki Positive staining twiki PlasticCoatedGrid twiki PioloformGrids? twiki Carbon Coating instructions twiki Carbon Coating using Thread twiki Carbon Coating using Carbon Rod twiki Metal Shadowing twiki
Overview of software in use CemProtocProcessoverview
Freeze Substitution Protocol twiki Freeze Substitution twiki
Helical Processing : Initial steps HelicalProcessing

Image Processing and computing

Helical Reconstruction with EmIP HelicalReconstruction
Overview of software in use twiki
Processing - tomographic data CemProtocProcessET
Description of EMIP, a GUI for various image processing techniques twiki Processing - electron crystallography twiki Processing - tomographic data twiki
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Processing - Helical Reconstruction twiki Processing - Single particle analysis twiki Background - single particle analysis Background - single particle analysis (from twiki) Electron Crystallography twiki Electron tomography protocols twiki
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Making Movies from Amira AmiraMovie

Courses

Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub

General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact BillRice or EdEng.

-- EdEng - 17 May 2012

Revision 517 May 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Contents

Overview

Interested in Cryoem? Cryoem at NYSBC General info on cryoem at NYSBC Cryoem Operations committee twiki EM as a technique in structural biology EM as a technique in structural biology (from twiki) Main cryoem page Publications related to CEM at NYSBC How to sign up for CEM equipment at NYSBC twiki
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
The site map you are now viewing CemSiteMap

Equipment

Equipment -- sample prep Equipment -- main plasma cleaner for glow discharge Plunge freezing equipment GlowDischarge Using Edwards Evaporator twiki Edwards Vacuum Evaporator overview twiki HpfSupplies twiki High Pressure Freezer twiki HpfUse twiki WohlwendUse twiki PressureRegulator twiki Preparation of microtome for cryo-sectioning twiki Use of the Oscilloscope/ Matlab twiki

Microscopes

Main page for all Microscopes Another page for all microscopes twiki CemParameters twiki jeol 1230 description Jeol1230Instructions twiki Jeol1230Information twiki Jeol1230 filament exchange instructions twiki jeol 2100 description Jeol2100Information twiki Jeol2100Basicinstructions twiki Jeol2100Instructions twiki jeol 3200 description Jeol3200Information twiki Jeol3200Basicinstructions twiki Jeol3200Instructions twiki How to collect dual tilt tomograms on Jeol3200 twiki Tecnai F20 description TecnaiInformation twiki TecnaiInstructions twiki Tecnai advanced instructions twiki F20 daily checklist twiki CcdBlankEnable, specific for Tecnai F20 twiki Microscope Shut Down twiki How to Find The Beam twiki How to Insert a Room Temperature Sample twiki How to Insert a CryoSample? twiki General Instructions for using cryo-holders twiki How to take a CCD image with Tietz software twiki How to take a film image twiki

Automated Data Collection

Automated data collection with SerialEM twiki Older notes on SerialEM twiki Notes on Shutter Box settings on Tecnai on Low Dose and SerialEM twiki SerialEM - notes on montages and use of the Navigator twiki Notes on Cem Robotics using JEOL1230 twiki Checklist before using 1230 Robot twiki Film Related Film Screening And Scanning Overview twiki Scanning - PDS Densitometer twiki Scanning - Zeiss Densitometer twiki Screening films with Optical Bench twiki Courses Graduate level course in cryo-EM Other seminars and courses in Cryo-EM twiki Previous EM Journal Clubs twiki

Lab Protocols

Main protocols page twiki Plunge freezing protocols Grid prep - homemade holey carbon (Claudio) twiki Grid prep - carbon sandwich twiki Grid prep - adding fiducial markers twiki Grid prep - general information twiki Grid prep - solid carbon films twiki Grid prep - homemade holey carbon (triafol) twiki high pressure freezing twiki
Notes on cryo sectioning Chyongere
Notes on cryo sectioning twiki Plunge freezing Theory Plunge freezing Theory(from twiki) twiki Plunge Freezing Practical(from twiki) twiki Staining twiki Negative staining twiki Positive staining twiki PlasticCoatedGrid twiki PioloformGrids? twiki Carbon Coating instructions twiki Carbon Coating using Thread twiki Carbon Coating using Carbon Rod twiki Metal Shadowing twiki
Overview of software in use CemProtocProcessoverview
Freeze Substitution Protocol twiki Freeze Substitution twiki
Helical Processing : Initial steps HelicalProcessing
Changed:
<
<

Image Processing

>
>

Image Processing and computing

 
Helical Reconstruction with EmIP HelicalReconstruction
Overview of software in use twiki
Processing - tomographic data CemProtocProcessET
Description of EMIP, a GUI for various image processing techniques twiki Processing - electron crystallography twiki Processing - tomographic data twiki
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Processing - Helical Reconstruction twiki Processing - Single particle analysis twiki Background - single particle analysis Background - single particle analysis (from twiki) Electron Crystallography twiki Electron tomography protocols twiki
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Added:
>
>
Making Movies from Amira AmiraMovie

Courses

 
Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub

General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact BillRice or EdEng.

-- EdEng - 17 May 2012

Revision 417 May 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Contents

Overview

Interested in Cryoem? Cryoem at NYSBC General info on cryoem at NYSBC Cryoem Operations committee twiki EM as a technique in structural biology EM as a technique in structural biology (from twiki) Main cryoem page Publications related to CEM at NYSBC How to sign up for CEM equipment at NYSBC twiki
Changed:
<
<
CEM staff at NYSBC (newer) CEM staff at NYSBC The site map you are now viewing
>
>
CEM staff at NYSBC CemStaff
Jobs available TemimpsJobs
The site map you are now viewing CemSiteMap
 

Equipment

Equipment -- sample prep Equipment -- main plasma cleaner for glow discharge Plunge freezing equipment GlowDischarge Using Edwards Evaporator twiki Edwards Vacuum Evaporator overview twiki HpfSupplies twiki High Pressure Freezer twiki HpfUse twiki WohlwendUse twiki PressureRegulator twiki Preparation of microtome for cryo-sectioning twiki Use of the Oscilloscope/ Matlab twiki

Microscopes

Main page for all Microscopes Another page for all microscopes twiki CemParameters twiki jeol 1230 description Jeol1230Instructions twiki Jeol1230Information twiki Jeol1230 filament exchange instructions twiki jeol 2100 description Jeol2100Information twiki Jeol2100Basicinstructions twiki Jeol2100Instructions twiki jeol 3200 description Jeol3200Information twiki Jeol3200Basicinstructions twiki Jeol3200Instructions twiki How to collect dual tilt tomograms on Jeol3200 twiki Tecnai F20 description TecnaiInformation twiki TecnaiInstructions twiki Tecnai advanced instructions twiki F20 daily checklist twiki CcdBlankEnable, specific for Tecnai F20 twiki Microscope Shut Down twiki How to Find The Beam twiki How to Insert a Room Temperature Sample twiki How to Insert a CryoSample? twiki General Instructions for using cryo-holders twiki How to take a CCD image with Tietz software twiki How to take a film image twiki

Automated Data Collection

Automated data collection with SerialEM twiki Older notes on SerialEM twiki Notes on Shutter Box settings on Tecnai on Low Dose and SerialEM twiki SerialEM - notes on montages and use of the Navigator twiki Notes on Cem Robotics using JEOL1230 twiki Checklist before using 1230 Robot twiki Film Related Film Screening And Scanning Overview twiki Scanning - PDS Densitometer twiki Scanning - Zeiss Densitometer twiki Screening films with Optical Bench twiki Courses Graduate level course in cryo-EM Other seminars and courses in Cryo-EM twiki Previous EM Journal Clubs twiki

Lab Protocols

Main protocols page twiki Plunge freezing protocols Grid prep - homemade holey carbon (Claudio) twiki Grid prep - carbon sandwich twiki Grid prep - adding fiducial markers twiki Grid prep - general information twiki Grid prep - solid carbon films twiki Grid prep - homemade holey carbon (triafol) twiki high pressure freezing twiki
Notes on cryo sectioning Chyongere
Notes on cryo sectioning twiki Plunge freezing Theory Plunge freezing Theory(from twiki) twiki Plunge Freezing Practical(from twiki) twiki Staining twiki Negative staining twiki Positive staining twiki PlasticCoatedGrid twiki PioloformGrids? twiki Carbon Coating instructions twiki Carbon Coating using Thread twiki Carbon Coating using Carbon Rod twiki Metal Shadowing twiki
Overview of software in use CemProtocProcessoverview
Freeze Substitution Protocol twiki Freeze Substitution twiki
Helical Processing : Initial steps HelicalProcessing

Image Processing

Helical Reconstruction with EmIP HelicalReconstruction
Overview of software in use twiki
Processing - tomographic data CemProtocProcessET
Description of EMIP, a GUI for various image processing techniques twiki Processing - electron crystallography twiki Processing - tomographic data twiki
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Processing - Helical Reconstruction twiki Processing - Single particle analysis twiki Background - single particle analysis Background - single particle analysis (from twiki) Electron Crystallography twiki Electron tomography protocols twiki
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub

General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact BillRice or EdEng.

-- EdEng - 17 May 2012

Revision 317 May 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Contents
Deleted:
<
<

General Info

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. If you have added any pages to be mirrored on the website from the twiki please contact BillRice or EdEng, or add it to the twiki page to update the site map.

d129 5

 

Overview

Interested in Cryoem? Cryoem at NYSBC General info on cryoem at NYSBC Cryoem Operations committee twiki EM as a technique in structural biology EM as a technique in structural biology (from twiki) Main cryoem page Publications related to CEM at NYSBC How to sign up for CEM equipment at NYSBC twiki CEM staff at NYSBC (newer) CEM staff at NYSBC The site map you are now viewing

Equipment

Equipment -- sample prep Equipment -- main plasma cleaner for glow discharge Plunge freezing equipment GlowDischarge Using Edwards Evaporator twiki Edwards Vacuum Evaporator overview twiki HpfSupplies twiki High Pressure Freezer twiki HpfUse twiki WohlwendUse twiki PressureRegulator twiki Preparation of microtome for cryo-sectioning twiki Use of the Oscilloscope/ Matlab twiki

Microscopes

Main page for all Microscopes Another page for all microscopes twiki CemParameters twiki jeol 1230 description Jeol1230Instructions twiki Jeol1230Information twiki Jeol1230 filament exchange instructions twiki jeol 2100 description Jeol2100Information twiki Jeol2100Basicinstructions twiki Jeol2100Instructions twiki jeol 3200 description Jeol3200Information twiki Jeol3200Basicinstructions twiki Jeol3200Instructions twiki How to collect dual tilt tomograms on Jeol3200 twiki Tecnai F20 description TecnaiInformation twiki TecnaiInstructions twiki Tecnai advanced instructions twiki F20 daily checklist twiki CcdBlankEnable, specific for Tecnai F20 twiki Microscope Shut Down twiki How to Find The Beam twiki How to Insert a Room Temperature Sample twiki How to Insert a CryoSample? twiki General Instructions for using cryo-holders twiki How to take a CCD image with Tietz software twiki How to take a film image twiki

Automated Data Collection

Automated data collection with SerialEM twiki Older notes on SerialEM twiki Notes on Shutter Box settings on Tecnai on Low Dose and SerialEM twiki SerialEM - notes on montages and use of the Navigator twiki Notes on Cem Robotics using JEOL1230 twiki Checklist before using 1230 Robot twiki Film Related Film Screening And Scanning Overview twiki Scanning - PDS Densitometer twiki Scanning - Zeiss Densitometer twiki Screening films with Optical Bench twiki Courses Graduate level course in cryo-EM Other seminars and courses in Cryo-EM twiki Previous EM Journal Clubs twiki

Lab Protocols

Main protocols page twiki Plunge freezing protocols Grid prep - homemade holey carbon (Claudio) twiki Grid prep - carbon sandwich twiki Grid prep - adding fiducial markers twiki Grid prep - general information twiki Grid prep - solid carbon films twiki Grid prep - homemade holey carbon (triafol) twiki high pressure freezing twiki
Notes on cryo sectioning Chyongere
Notes on cryo sectioning twiki Plunge freezing Theory Plunge freezing Theory(from twiki) twiki Plunge Freezing Practical(from twiki) twiki Staining twiki Negative staining twiki Positive staining twiki PlasticCoatedGrid twiki PioloformGrids? twiki Carbon Coating instructions twiki Carbon Coating using Thread twiki Carbon Coating using Carbon Rod twiki Metal Shadowing twiki
Overview of software in use CemProtocProcessoverview
Freeze Substitution Protocol twiki Freeze Substitution twiki
Helical Processing : Initial steps HelicalProcessing

Image Processing

Helical Reconstruction with EmIP HelicalReconstruction
Overview of software in use twiki
Processing - tomographic data CemProtocProcessET
Description of EMIP, a GUI for various image processing techniques twiki Processing - electron crystallography twiki Processing - tomographic data twiki
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Processing - Helical Reconstruction twiki Processing - Single particle analysis twiki Background - single particle analysis Background - single particle analysis (from twiki) Electron Crystallography twiki Electron tomography protocols twiki
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Graduate level course in cryo-EM CemCourseAnnouncement
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub

General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact BillRice or EdEng.

-- EdEng - 17 May 2012

Revision 217 May 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Contents
Changed:
<
<
If you have added any pages to be mirrored on the website from the twiki please contact EdEng to update the site map.
>
>

General Info

 
Changed:
<
<

Name of the topic

>
>
This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. If you have added any pages to be mirrored on the website from the twiki please contact BillRice or EdEng, or add it to the twiki page to update the site map.
Deleted:
<
<

Sublevel topic

subsub level topic

 
Added:
>
>
d129 5

Overview

Interested in Cryoem? Cryoem at NYSBC General info on cryoem at NYSBC Cryoem Operations committee twiki EM as a technique in structural biology EM as a technique in structural biology (from twiki) Main cryoem page Publications related to CEM at NYSBC How to sign up for CEM equipment at NYSBC twiki CEM staff at NYSBC (newer) CEM staff at NYSBC The site map you are now viewing

Equipment

Equipment -- sample prep Equipment -- main plasma cleaner for glow discharge Plunge freezing equipment GlowDischarge Using Edwards Evaporator twiki Edwards Vacuum Evaporator overview twiki HpfSupplies twiki High Pressure Freezer twiki HpfUse twiki WohlwendUse twiki PressureRegulator twiki Preparation of microtome for cryo-sectioning twiki Use of the Oscilloscope/ Matlab twiki

Microscopes

Main page for all Microscopes Another page for all microscopes twiki CemParameters twiki jeol 1230 description Jeol1230Instructions twiki Jeol1230Information twiki Jeol1230 filament exchange instructions twiki jeol 2100 description Jeol2100Information twiki Jeol2100Basicinstructions twiki Jeol2100Instructions twiki jeol 3200 description Jeol3200Information twiki Jeol3200Basicinstructions twiki Jeol3200Instructions twiki How to collect dual tilt tomograms on Jeol3200 twiki Tecnai F20 description TecnaiInformation twiki TecnaiInstructions twiki Tecnai advanced instructions twiki F20 daily checklist twiki CcdBlankEnable, specific for Tecnai F20 twiki Microscope Shut Down twiki How to Find The Beam twiki How to Insert a Room Temperature Sample twiki How to Insert a CryoSample? twiki General Instructions for using cryo-holders twiki How to take a CCD image with Tietz software twiki How to take a film image twiki

Automated Data Collection

Automated data collection with SerialEM twiki Older notes on SerialEM twiki Notes on Shutter Box settings on Tecnai on Low Dose and SerialEM twiki SerialEM - notes on montages and use of the Navigator twiki Notes on Cem Robotics using JEOL1230 twiki Checklist before using 1230 Robot twiki Film Related Film Screening And Scanning Overview twiki Scanning - PDS Densitometer twiki Scanning - Zeiss Densitometer twiki Screening films with Optical Bench twiki Courses Graduate level course in cryo-EM Other seminars and courses in Cryo-EM twiki Previous EM Journal Clubs twiki

Lab Protocols

Main protocols page twiki Plunge freezing protocols Grid prep - homemade holey carbon (Claudio) twiki Grid prep - carbon sandwich twiki Grid prep - adding fiducial markers twiki Grid prep - general information twiki Grid prep - solid carbon films twiki Grid prep - homemade holey carbon (triafol) twiki high pressure freezing twiki
Notes on cryo sectioning Chyongere
Notes on cryo sectioning twiki Plunge freezing Theory Plunge freezing Theory(from twiki) twiki Plunge Freezing Practical(from twiki) twiki Staining twiki Negative staining twiki Positive staining twiki PlasticCoatedGrid twiki PioloformGrids? twiki Carbon Coating instructions twiki Carbon Coating using Thread twiki Carbon Coating using Carbon Rod twiki Metal Shadowing twiki
Overview of software in use CemProtocProcessoverview
Freeze Substitution Protocol twiki Freeze Substitution twiki
Helical Processing : Initial steps HelicalProcessing

Image Processing

Helical Reconstruction with EmIP HelicalReconstruction
Overview of software in use twiki
Processing - tomographic data CemProtocProcessET
Description of EMIP, a GUI for various image processing techniques twiki Processing - electron crystallography twiki Processing - tomographic data twiki
Spider processing on cluster SpiderRefinement
EMAN refinement CemEmanRefinement
Processing - Helical Reconstruction twiki Processing - Single particle analysis twiki Background - single particle analysis Background - single particle analysis (from twiki) Electron Crystallography twiki Electron tomography protocols twiki
Notes on getting a 8-bit display in Linux DisplayDepths
Install Python InstallwxPython
Making Movies in linux MovieMaking
Graduate level course in cryo-EM CemCourseAnnouncement
 
Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub

General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact BillRice or EdEng.

-- EdEng - 17 May 2012

Revision 117 May 2012 - Main.EdEng

 
META TOPICPARENT name="CemTwikiToWebMainPage"
Contents

If you have added any pages to be mirrored on the website from the twiki please contact EdEng to update the site map.

Name of the topic

Sublevel topic

subsub level topic

Other seminars and courses in Cryo-EM CemSeminarsCourses
Previous EM Journal Clubs PastEMJournalClub

General info about this sitemap

This sitemap is dynamically updated from the twiki page CemSiteMap. However, additions have to be manually entered. If you have added any pages to be mirrored from the twiki, or would like to have a public mirror of a twiki page, please contact BillRice or EdEng.

-- EdEng - 17 May 2012

 
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