Difference: CemSiteMap (27 vs. 28)

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
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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.

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