Difference: GatlingGun (1 vs. 26)

Revision 2604 Apr 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows (note: program does not need to be run)
    j1230-temextreg.png
  • Settings in TemServer 20xx (visible when viewing Properties) are :
    j1230-temserver20xx.png

Digital Micrograph communication with microscope

  • Digital Micrograph communicates with J1230 through serial port by default
  • Setup is as follows:
    microscope-setup-normal.png
  • When emulator is running, can optionally use JEOL COM as microscope rather than JEOL 12n0
    microscope-setup-emulated.png
  • In either option, there is a test panel for testing Digital Micrograph's ability to control microscope
    microscope-setup-test.png

  • Testing of commands in Digital Micrograph
Command Working in J12n0 mode Working in Temcon emulated mode
Get beam energy yes yes
Get camera length failed return 0
Get Illumination mode failed  
Get Image Optics mode yes  
Get mag yes no
Set mag no no
Get spot size failed no
Set spot size failed no
Get Brightness yes yes
Set Brightness yes no
Get Focus yes  
Change Focus yes
Get Objective Stig yes  
Change Objective Stig yes
Get Beam Shift yes  
Change Beam Shift yes  
Get Beam Tilt yes  
Change Beam Tilt yes  
Get C Stig yes  
Change C Stig yes  
Get Image Shift yes  
Change Image Shift yes  

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60

Leginon Installation

  • Will be using version 1.5 of Leginon
Changed:
<
<
  • TO BE DONE:
    • Install NumExtension 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box
>
>
  • DONE:
    • Installed NumExtension 1.1.0
    • Installed pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Installed sinedon -r39
    • Installed pyami - r69
    • Installed Imageviewer
    • Installed Leginon - r5457
    • Edited default.cfg to configure Leginon to communicate with proper database
    • Edited sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box
Added:
>
>
    • Communicates with camera, but complains about size

Testing of python control of microscope
 

Serialport in python

  • Loaded serialpy library
  • works to control serial port
  • Currently need to run it using IDLE
  • To be done
    • Test all commands in jeol_1230_computer control manual
    • Write a simple comnmand-line interface to control scope
    • implement commands in pyscope leginon module
    • Testing of commands using serial port control
Command Code Result

  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

* jeol_1230_computer.pdf: serial port command instructions for jeol 1230

META FILEATTACHMENT attr="" autoattached="1" comment="serial port command instructions for jeol 1230" date="1206396439" name="jeol_1230_computer.pdf" path="jeol_1230_computer.pdf" size="15093571" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-normal communication" date="1206394754" name="microscope-setup-normal.png" path="microscope-setup-normal.png" size="14580" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-test panel" date="1206394808" name="microscope-setup-test.png" path="microscope-setup-test.png" size="32840" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm - emulated communication" date="1206394786" name="microscope-setup-emulated.png" path="microscope-setup-emulated.png" size="15155" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206454293" name="j1230-temextreg.png" path="j1230-temextreg.png" size="12366" user="Main.BillRice" version=""
META TOPICMOVED by="DavidStokes" date="1206448294" from="Main.GatlanGun" to="Main.GatlingGun"

Revision 2527 Mar 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows (note: program does not need to be run)
    j1230-temextreg.png
  • Settings in TemServer 20xx (visible when viewing Properties) are :
    j1230-temserver20xx.png

Digital Micrograph communication with microscope

  • Digital Micrograph communicates with J1230 through serial port by default
  • Setup is as follows:
    microscope-setup-normal.png
  • When emulator is running, can optionally use JEOL COM as microscope rather than JEOL 12n0
    microscope-setup-emulated.png
  • In either option, there is a test panel for testing Digital Micrograph's ability to control microscope
    microscope-setup-test.png

  • Testing of commands in Digital Micrograph
Command Working in J12n0 mode Working in Temcon emulated mode
Get beam energy yes yes
Changed:
<
<
Get camera length return 0 return 0
Getmag yes no
Set mag yes no
Get spot size no no
Set spot size no no
>
>
Get camera length failed return 0
Get Illumination mode failed  
Get Image Optics mode yes  
Get mag yes no
Set mag no no
Added:
>
>
Get spot size failed no
Set spot size failed no
 
Get Brightness yes yes
Set Brightness yes no
Added:
>
>
Get Focus yes  
Change Focus yes
Get Objective Stig yes  
Change Objective Stig yes
Get Beam Shift yes  
Change Beam Shift yes  
Get Beam Tilt yes  
Change Beam Tilt yes  
Get C Stig yes  
Change C Stig yes  
Get Image Shift yes  
Change Image Shift yes  
 

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60

Leginon Installation

  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box

Serialport in python

  • Loaded serialpy library
  • works to control serial port
  • Currently need to run it using IDLE
  • To be done
    • Test all commands in jeol_1230_computer control manual
    • Write a simple comnmand-line interface to control scope
    • implement commands in pyscope leginon module
    • Testing of commands using serial port control
Command Code Result

  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

* jeol_1230_computer.pdf: serial port command instructions for jeol 1230

META FILEATTACHMENT attr="" autoattached="1" comment="serial port command instructions for jeol 1230" date="1206396439" name="jeol_1230_computer.pdf" path="jeol_1230_computer.pdf" size="15093571" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-normal communication" date="1206394754" name="microscope-setup-normal.png" path="microscope-setup-normal.png" size="14580" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-test panel" date="1206394808" name="microscope-setup-test.png" path="microscope-setup-test.png" size="32840" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm - emulated communication" date="1206394786" name="microscope-setup-emulated.png" path="microscope-setup-emulated.png" size="15155" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206454293" name="j1230-temextreg.png" path="j1230-temextreg.png" size="12366" user="Main.BillRice" version=""
META TOPICMOVED by="DavidStokes" date="1206448294" from="Main.GatlanGun" to="Main.GatlingGun"

Revision 2425 Mar 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows (note: program does not need to be run)
    j1230-temextreg.png
  • Settings in TemServer 20xx (visible when viewing Properties) are :
    j1230-temserver20xx.png

Digital Micrograph communication with microscope

  • Digital Micrograph communicates with J1230 through serial port by default
  • Setup is as follows:
    microscope-setup-normal.png
  • When emulator is running, can optionally use JEOL COM as microscope rather than JEOL 12n0
    microscope-setup-emulated.png
  • In either option, there is a test panel for testing Digital Micrograph's ability to control microscope
    microscope-setup-test.png

  • Testing of commands in Digital Micrograph
Command Working in J12n0 mode Working in Temcon emulated mode
Get beam energy yes yes
Get camera length return 0 return 0
Getmag yes no
Set mag yes no
Get spot size no no
Set spot size no no
Added:
>
>
Get Brightness yes yes
Set Brightness yes no
 

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60

Leginon Installation

  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box

Serialport in python

  • Loaded serialpy library
  • works to control serial port
  • Currently need to run it using IDLE
  • To be done
    • Test all commands in jeol_1230_computer control manual
    • Write a simple comnmand-line interface to control scope
    • implement commands in pyscope leginon module
    • Testing of commands using serial port control
Command Code Result

  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

* jeol_1230_computer.pdf: serial port command instructions for jeol 1230

META FILEATTACHMENT attr="" autoattached="1" comment="serial port command instructions for jeol 1230" date="1206396439" name="jeol_1230_computer.pdf" path="jeol_1230_computer.pdf" size="15093571" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-normal communication" date="1206394754" name="microscope-setup-normal.png" path="microscope-setup-normal.png" size="14580" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-test panel" date="1206394808" name="microscope-setup-test.png" path="microscope-setup-test.png" size="32840" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm - emulated communication" date="1206394786" name="microscope-setup-emulated.png" path="microscope-setup-emulated.png" size="15155" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206454293" name="j1230-temextreg.png" path="j1230-temextreg.png" size="12366" user="Main.BillRice" version=""
META TOPICMOVED by="DavidStokes" date="1206448294" from="Main.GatlanGun" to="Main.GatlingGun"

Revision 2325 Mar 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
Changed:
<
<
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows
>
>
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows (note: program does not need to be run)
  j1230-temextreg.png
Changed:
<
<
  • Settings in TemServer? 20xx (visible when viewing Properties) are :
>
>
  • Settings in TemServer 20xx (visible when viewing Properties) are :
  j1230-temserver20xx.png

Digital Micrograph communication with microscope

  • Digital Micrograph communicates with J1230 through serial port by default
  • Setup is as follows:
    microscope-setup-normal.png
  • When emulator is running, can optionally use JEOL COM as microscope rather than JEOL 12n0
    microscope-setup-emulated.png
  • In either option, there is a test panel for testing Digital Micrograph's ability to control microscope
    microscope-setup-test.png

  • Testing of commands in Digital Micrograph
Changed:
<
<
Command Working in J12n0 mode Working in Temcon emulated mode
>
>
Command Working in J12n0 mode Working in Temcon emulated mode
 
Get beam energy yes yes
Get camera length return 0 return 0
Changed:
<
<
Getmag yes no
Set mag yes no
Get spot size no no
>
>
Getmag yes no
Set mag yes no
Get spot size no no
 
Set spot size no no

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
Changed:
<
<
    • install MySQL? python client
>
>
    • install MySQL python client
 
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60

Leginon Installation

  • Will be using version 1.5 of Leginon
  • TO BE DONE:
Changed:
<
<
    • Install NumExtension? 1.1.0
>
>
    • Install NumExtension 1.1.0
 
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box

Serialport in python

  • Loaded serialpy library
  • works to control serial port
  • Currently need to run it using IDLE
  • To be done
    • Test all commands in jeol_1230_computer control manual
    • Write a simple comnmand-line interface to control scope
    • implement commands in pyscope leginon module
    • Testing of commands using serial port control
Changed:
<
<
Command Code Result
>
>
Command Code Result
 
  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

* jeol_1230_computer.pdf: serial port command instructions for jeol 1230

META FILEATTACHMENT attr="" autoattached="1" comment="serial port command instructions for jeol 1230" date="1206396439" name="jeol_1230_computer.pdf" path="jeol_1230_computer.pdf" size="15093571" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-normal communication" date="1206394754" name="microscope-setup-normal.png" path="microscope-setup-normal.png" size="14580" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-test panel" date="1206394808" name="microscope-setup-test.png" path="microscope-setup-test.png" size="32840" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm - emulated communication" date="1206394786" name="microscope-setup-emulated.png" path="microscope-setup-emulated.png" size="15155" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206454293" name="j1230-temextreg.png" path="j1230-temextreg.png" size="12366" user="Main.BillRice" version=""
META TOPICMOVED by="DavidStokes" date="1206448294" from="Main.GatlanGun" to="Main.GatlingGun"

Revision 2225 Mar 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows
    j1230-temextreg.png
  • Settings in TemServer? 20xx (visible when viewing Properties) are :
    j1230-temserver20xx.png

Digital Micrograph communication with microscope

  • Digital Micrograph communicates with J1230 through serial port by default
  • Setup is as follows:
    microscope-setup-normal.png
  • When emulator is running, can optionally use JEOL COM as microscope rather than JEOL 12n0
    microscope-setup-emulated.png
  • In either option, there is a test panel for testing Digital Micrograph's ability to control microscope
    microscope-setup-test.png

  • Testing of commands in Digital Micrograph
Command Working in J12n0 mode Working in Temcon emulated mode
Get beam energy yes yes
Get camera length return 0 return 0
Getmag yes no
Set mag yes no
Get spot size no no
Set spot size no no

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL? python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60

Leginon Installation

  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension? 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box

Serialport in python

  • Loaded serialpy library
  • works to control serial port
  • Currently need to run it using IDLE
  • To be done
Added:
>
>
    • Testing of commands using serial port control
Command Code Result
 
  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

* jeol_1230_computer.pdf: serial port command instructions for jeol 1230

META FILEATTACHMENT attr="" autoattached="1" comment="serial port command instructions for jeol 1230" date="1206396439" name="jeol_1230_computer.pdf" path="jeol_1230_computer.pdf" size="15093571" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-normal communication" date="1206394754" name="microscope-setup-normal.png" path="microscope-setup-normal.png" size="14580" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-test panel" date="1206394808" name="microscope-setup-test.png" path="microscope-setup-test.png" size="32840" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm - emulated communication" date="1206394786" name="microscope-setup-emulated.png" path="microscope-setup-emulated.png" size="15155" user="Main.BillRice" version=""
Changed:
<
<
META FILEATTACHMENT attachment="j1230-temextreg.png" attr="" comment="temserver20xx settings" date="1206454293" name="j1230-temextreg.png" path="j1230-temextreg.png" size="12366" stream="j1230-temextreg.png" user="Main.BillRice" version="0"
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206454293" name="j1230-temextreg.png" path="j1230-temextreg.png" size="12366" user="Main.BillRice" version=""
 
META TOPICMOVED by="DavidStokes" date="1206448294" from="Main.GatlanGun" to="Main.GatlingGun"

Revision 2125 Mar 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows
    j1230-temextreg.png
  • Settings in TemServer? 20xx (visible when viewing Properties) are :
    j1230-temserver20xx.png

Digital Micrograph communication with microscope

  • Digital Micrograph communicates with J1230 through serial port by default
  • Setup is as follows:
    microscope-setup-normal.png
  • When emulator is running, can optionally use JEOL COM as microscope rather than JEOL 12n0
    microscope-setup-emulated.png
  • In either option, there is a test panel for testing Digital Micrograph's ability to control microscope
    microscope-setup-test.png

  • Testing of commands in Digital Micrograph
Command Working in J12n0 mode Working in Temcon emulated mode
Get beam energy yes yes
Get camera length return 0 return 0
Getmag yes no
Set mag yes no
Get spot size no no
Set spot size no no

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL? python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60

Leginon Installation

  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension? 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box

Serialport in python

  • Loaded serialpy library
  • works to control serial port
  • Currently need to run it using IDLE
  • To be done

  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

* jeol_1230_computer.pdf: serial port command instructions for jeol 1230

META FILEATTACHMENT attr="" autoattached="1" comment="serial port command instructions for jeol 1230" date="1206396439" name="jeol_1230_computer.pdf" path="jeol_1230_computer.pdf" size="15093571" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-normal communication" date="1206394754" name="microscope-setup-normal.png" path="microscope-setup-normal.png" size="14580" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-test panel" date="1206394808" name="microscope-setup-test.png" path="microscope-setup-test.png" size="32840" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm - emulated communication" date="1206394786" name="microscope-setup-emulated.png" path="microscope-setup-emulated.png" size="15155" user="Main.BillRice" version=""
Changed:
<
<
META FILEATTACHMENT attr="" autoattached="1" comment="temextreg window" date="1206389445" name="j1230-temextreg.png" path="j1230-temextreg.png" size="11424" user="Main.BillRice" version=""
>
>
META FILEATTACHMENT attachment="j1230-temextreg.png" attr="" comment="temserver20xx settings" date="1206454293" name="j1230-temextreg.png" path="j1230-temextreg.png" size="12366" stream="j1230-temextreg.png" user="Main.BillRice" version="0"
 
META TOPICMOVED by="DavidStokes" date="1206448294" from="Main.GatlanGun" to="Main.GatlingGun"

Revision 2025 Mar 2008 - Main.DavidStokes

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows
    j1230-temextreg.png
  • Settings in TemServer? 20xx (visible when viewing Properties) are :
    j1230-temserver20xx.png

Digital Micrograph communication with microscope

  • Digital Micrograph communicates with J1230 through serial port by default
  • Setup is as follows:
    microscope-setup-normal.png
  • When emulator is running, can optionally use JEOL COM as microscope rather than JEOL 12n0
    microscope-setup-emulated.png
  • In either option, there is a test panel for testing Digital Micrograph's ability to control microscope
    microscope-setup-test.png

  • Testing of commands in Digital Micrograph
Command Working in J12n0 mode Working in Temcon emulated mode
Get beam energy yes yes
Get camera length return 0 return 0
Getmag yes no
Set mag yes no
Get spot size no no
Set spot size no no

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL? python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60

Leginon Installation

  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension? 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box

Serialport in python

  • Loaded serialpy library
  • works to control serial port
  • Currently need to run it using IDLE
  • To be done

  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

* jeol_1230_computer.pdf: serial port command instructions for jeol 1230

META FILEATTACHMENT attr="" autoattached="1" comment="serial port command instructions for jeol 1230" date="1206396439" name="jeol_1230_computer.pdf" path="jeol_1230_computer.pdf" size="15093571" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-normal communication" date="1206394754" name="microscope-setup-normal.png" path="microscope-setup-normal.png" size="14580" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-test panel" date="1206394808" name="microscope-setup-test.png" path="microscope-setup-test.png" size="32840" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm - emulated communication" date="1206394786" name="microscope-setup-emulated.png" path="microscope-setup-emulated.png" size="15155" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temextreg window" date="1206389445" name="j1230-temextreg.png" path="j1230-temextreg.png" size="11424" user="Main.BillRice" version=""
Added:
>
>
META TOPICMOVED by="DavidStokes" date="1206448294" from="Main.GatlanGun" to="Main.GatlingGun"
 

Revision 1924 Mar 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows
    j1230-temextreg.png
  • Settings in TemServer? 20xx (visible when viewing Properties) are :
    j1230-temserver20xx.png

Digital Micrograph communication with microscope

  • Digital Micrograph communicates with J1230 through serial port by default
  • Setup is as follows:
    microscope-setup-normal.png
  • When emulator is running, can optionally use JEOL COM as microscope rather than JEOL 12n0
    microscope-setup-emulated.png
  • In either option, there is a test panel for testing Digital Micrograph's ability to control microscope
    microscope-setup-test.png

  • Testing of commands in Digital Micrograph
Command Working in J12n0 mode Working in Temcon emulated mode
Get beam energy yes yes
Added:
>
>
Get camera length return 0 return 0
 
Getmag yes no
Set mag yes no
Get spot size no no
Set spot size no no

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL? python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60

Leginon Installation

  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension? 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box

Serialport in python

  • Loaded serialpy library
  • works to control serial port
  • Currently need to run it using IDLE
  • To be done

  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

* jeol_1230_computer.pdf: serial port command instructions for jeol 1230

META FILEATTACHMENT attr="" autoattached="1" comment="serial port command instructions for jeol 1230" date="1206396439" name="jeol_1230_computer.pdf" path="jeol_1230_computer.pdf" size="15093571" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-normal communication" date="1206394754" name="microscope-setup-normal.png" path="microscope-setup-normal.png" size="14580" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-test panel" date="1206394808" name="microscope-setup-test.png" path="microscope-setup-test.png" size="32840" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm - emulated communication" date="1206394786" name="microscope-setup-emulated.png" path="microscope-setup-emulated.png" size="15155" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temextreg window" date="1206389445" name="j1230-temextreg.png" path="j1230-temextreg.png" size="11424" user="Main.BillRice" version=""

Revision 1824 Mar 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows
    j1230-temextreg.png
  • Settings in TemServer? 20xx (visible when viewing Properties) are :
    j1230-temserver20xx.png

Digital Micrograph communication with microscope

  • Digital Micrograph communicates with J1230 through serial port by default
  • Setup is as follows:
    microscope-setup-normal.png
  • When emulator is running, can optionally use JEOL COM as microscope rather than JEOL 12n0
    microscope-setup-emulated.png
  • In either option, there is a test panel for testing Digital Micrograph's ability to control microscope
    microscope-setup-test.png

  • Testing of commands in Digital Micrograph
Command Working in J12n0 mode Working in Temcon emulated mode
Added:
>
>
Get beam energy yes yes
 
Getmag yes no
Set mag yes no
Get spot size no no
Set spot size no no

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL? python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60

Leginon Installation

  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension? 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box

Serialport in python

  • Loaded serialpy library
  • works to control serial port
  • Currently need to run it using IDLE
  • To be done

  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

* jeol_1230_computer.pdf: serial port command instructions for jeol 1230

META FILEATTACHMENT attr="" autoattached="1" comment="serial port command instructions for jeol 1230" date="1206396439" name="jeol_1230_computer.pdf" path="jeol_1230_computer.pdf" size="15093571" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-normal communication" date="1206394754" name="microscope-setup-normal.png" path="microscope-setup-normal.png" size="14580" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-test panel" date="1206394808" name="microscope-setup-test.png" path="microscope-setup-test.png" size="32840" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm - emulated communication" date="1206394786" name="microscope-setup-emulated.png" path="microscope-setup-emulated.png" size="15155" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temextreg window" date="1206389445" name="j1230-temextreg.png" path="j1230-temextreg.png" size="11424" user="Main.BillRice" version=""

Revision 1724 Mar 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows
    j1230-temextreg.png
  • Settings in TemServer? 20xx (visible when viewing Properties) are :
    j1230-temserver20xx.png

Digital Micrograph communication with microscope

  • Digital Micrograph communicates with J1230 through serial port by default
  • Setup is as follows:
    microscope-setup-normal.png
  • When emulator is running, can optionally use JEOL COM as microscope rather than JEOL 12n0
    microscope-setup-emulated.png
  • In either option, there is a test panel for testing Digital Micrograph's ability to control microscope
    microscope-setup-test.png

  • Testing of commands in Digital Micrograph
Command Working in J12n0 mode Working in Temcon emulated mode
Getmag yes no
Set mag yes no
Get spot size no no
Set spot size no no

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL? python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60

Leginon Installation

  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension? 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box
Changed:
<
<		--+++ Serialport in python
>
>

Serialport in python

 
  • Loaded serialpy library
  • works to control serial port
  • Currently need to run it using IDLE
  • To be done

  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

* jeol_1230_computer.pdf: serial port command instructions for jeol 1230

META FILEATTACHMENT attr="" autoattached="1" comment="serial port command instructions for jeol 1230" date="1206396439" name="jeol_1230_computer.pdf" path="jeol_1230_computer.pdf" size="15093571" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-normal communication" date="1206394754" name="microscope-setup-normal.png" path="microscope-setup-normal.png" size="14580" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-test panel" date="1206394808" name="microscope-setup-test.png" path="microscope-setup-test.png" size="32840" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm - emulated communication" date="1206394786" name="microscope-setup-emulated.png" path="microscope-setup-emulated.png" size="15155" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temextreg window" date="1206389445" name="j1230-temextreg.png" path="j1230-temextreg.png" size="11424" user="Main.BillRice" version=""

Revision 1624 Mar 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows
    j1230-temextreg.png
  • Settings in TemServer? 20xx (visible when viewing Properties) are :
    j1230-temserver20xx.png

Digital Micrograph communication with microscope

  • Digital Micrograph communicates with J1230 through serial port by default
  • Setup is as follows:
    microscope-setup-normal.png
  • When emulator is running, can optionally use JEOL COM as microscope rather than JEOL 12n0
    microscope-setup-emulated.png
  • In either option, there is a test panel for testing Digital Micrograph's ability to control microscope
    microscope-setup-test.png

  • Testing of commands in Digital Micrograph
Command Working in J12n0 mode Working in Temcon emulated mode
Getmag yes no
Set mag yes no
Get spot size no no
Set spot size no no

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL? python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
Changed:
<
<
    • install scipy 0.60
>
>
    • install scipy 0.60
Added:
>
>
 

Leginon Installation

  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension? 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box

--+++ Serialport in python

  • Loaded serialpy library
  • works to control serial port
  • Currently need to run it using IDLE
  • To be done

  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

* jeol_1230_computer.pdf: serial port command instructions for jeol 1230

META FILEATTACHMENT attr="" autoattached="1" comment="serial port command instructions for jeol 1230" date="1206396439" name="jeol_1230_computer.pdf" path="jeol_1230_computer.pdf" size="15093571" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-normal communication" date="1206394754" name="microscope-setup-normal.png" path="microscope-setup-normal.png" size="14580" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-test panel" date="1206394808" name="microscope-setup-test.png" path="microscope-setup-test.png" size="32840" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm - emulated communication" date="1206394786" name="microscope-setup-emulated.png" path="microscope-setup-emulated.png" size="15155" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temextreg window" date="1206389445" name="j1230-temextreg.png" path="j1230-temextreg.png" size="11424" user="Main.BillRice" version=""

Revision 1524 Mar 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows
    j1230-temextreg.png
  • Settings in TemServer? 20xx (visible when viewing Properties) are :
    j1230-temserver20xx.png

Digital Micrograph communication with microscope

  • Digital Micrograph communicates with J1230 through serial port by default
  • Setup is as follows:
    microscope-setup-normal.png
  • When emulator is running, can optionally use JEOL COM as microscope rather than JEOL 12n0
    microscope-setup-emulated.png
  • In either option, there is a test panel for testing Digital Micrograph's ability to control microscope
    microscope-setup-test.png

  • Testing of commands in Digital Micrograph
Command Working in J12n0 mode Working in Temcon emulated mode
Getmag yes no
Set mag yes no
Get spot size no no
Set spot size no no

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL? python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60

Leginon Installation

  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension? 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box
Added:
>
>		--+++ Serialport in python
  • Loaded serialpy library
  • works to control serial port
  • Currently need to run it using IDLE
  • To be done
 
  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

* jeol_1230_computer.pdf: serial port command instructions for jeol 1230

META FILEATTACHMENT attr="" autoattached="1" comment="serial port command instructions for jeol 1230" date="1206396439" name="jeol_1230_computer.pdf" path="jeol_1230_computer.pdf" size="15093571" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-normal communication" date="1206394754" name="microscope-setup-normal.png" path="microscope-setup-normal.png" size="14580" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-test panel" date="1206394808" name="microscope-setup-test.png" path="microscope-setup-test.png" size="32840" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm - emulated communication" date="1206394786" name="microscope-setup-emulated.png" path="microscope-setup-emulated.png" size="15155" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temextreg window" date="1206389445" name="j1230-temextreg.png" path="j1230-temextreg.png" size="11424" user="Main.BillRice" version=""

Revision 1424 Mar 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows
    j1230-temextreg.png
  • Settings in TemServer? 20xx (visible when viewing Properties) are :
    j1230-temserver20xx.png

Digital Micrograph communication with microscope

  • Digital Micrograph communicates with J1230 through serial port by default
  • Setup is as follows:
    microscope-setup-normal.png
  • When emulator is running, can optionally use JEOL COM as microscope rather than JEOL 12n0
    microscope-setup-emulated.png
  • In either option, there is a test panel for testing Digital Micrograph's ability to control microscope
    microscope-setup-test.png

  • Testing of commands in Digital Micrograph
Command Working in J12n0 mode Working in Temcon emulated mode
Changed:
<
<
Getmag yes no
Set mag yes no
Get spot size no no
Set spot size no no
>
>
Getmag yes no
Set mag yes no
Get spot size no no
Set spot size no no
 

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL? python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60

Leginon Installation

  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension? 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box

  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

* jeol_1230_computer.pdf: serial port command instructions for jeol 1230

META FILEATTACHMENT attr="" autoattached="1" comment="serial port command instructions for jeol 1230" date="1206396439" name="jeol_1230_computer.pdf" path="jeol_1230_computer.pdf" size="15093571" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-normal communication" date="1206394754" name="microscope-setup-normal.png" path="microscope-setup-normal.png" size="14580" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-test panel" date="1206394808" name="microscope-setup-test.png" path="microscope-setup-test.png" size="32840" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm - emulated communication" date="1206394786" name="microscope-setup-emulated.png" path="microscope-setup-emulated.png" size="15155" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temextreg window" date="1206389445" name="j1230-temextreg.png" path="j1230-temextreg.png" size="11424" user="Main.BillRice" version=""

Revision 1324 Mar 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows
    j1230-temextreg.png
  • Settings in TemServer? 20xx (visible when viewing Properties) are :
    j1230-temserver20xx.png

Digital Micrograph communication with microscope

  • Digital Micrograph communicates with J1230 through serial port by default
  • Setup is as follows:
    microscope-setup-normal.png
  • When emulator is running, can optionally use JEOL COM as microscope rather than JEOL 12n0
    microscope-setup-emulated.png
  • In either option, there is a test panel for testing Digital Micrograph's ability to control microscope
    microscope-setup-test.png
Added:
>
>
  • Testing of commands in Digital Micrograph
Command Working in J12n0 mode Working in Temcon emulated mode
Getmag yes no
Set mag yes no
Get spot size no no
Set spot size no no
 

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL? python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60

Leginon Installation

  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension? 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box

  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

* jeol_1230_computer.pdf: serial port command instructions for jeol 1230

Added:
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="serial port command instructions for jeol 1230" date="1206396439" name="jeol_1230_computer.pdf" path="jeol_1230_computer.pdf" size="15093571" user="Main.BillRice" version=""
 
META FILEATTACHMENT attr="" autoattached="1" comment="dm-normal communication" date="1206394754" name="microscope-setup-normal.png" path="microscope-setup-normal.png" size="14580" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-test panel" date="1206394808" name="microscope-setup-test.png" path="microscope-setup-test.png" size="32840" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm - emulated communication" date="1206394786" name="microscope-setup-emulated.png" path="microscope-setup-emulated.png" size="15155" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temextreg window" date="1206389445" name="j1230-temextreg.png" path="j1230-temextreg.png" size="11424" user="Main.BillRice" version=""
Deleted:
<
<
META FILEATTACHMENT attachment="jeol_1230_computer.pdf" attr="" comment="serial port command instructions for jeol 1230" date="1206396439" name="jeol_1230_computer.pdf" path="jeol_1230_computer.pdf" size="15093571" stream="jeol_1230_computer.pdf" user="Main.BillRice" version="0"
 

Revision 1224 Mar 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows
    j1230-temextreg.png
  • Settings in TemServer? 20xx (visible when viewing Properties) are :
    j1230-temserver20xx.png

Digital Micrograph communication with microscope

  • Digital Micrograph communicates with J1230 through serial port by default
  • Setup is as follows:
    microscope-setup-normal.png
  • When emulator is running, can optionally use JEOL COM as microscope rather than JEOL 12n0
    microscope-setup-emulated.png
  • In either option, there is a test panel for testing Digital Micrograph's ability to control microscope
    microscope-setup-test.png

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL? python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60

Leginon Installation

  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension? 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box

  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

Added:
>
>		 * jeol_1230_computer.pdf: serial port command instructions for jeol 1230
 
META FILEATTACHMENT attr="" autoattached="1" comment="dm-normal communication" date="1206394754" name="microscope-setup-normal.png" path="microscope-setup-normal.png" size="14580" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm-test panel" date="1206394808" name="microscope-setup-test.png" path="microscope-setup-test.png" size="32840" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm - emulated communication" date="1206394786" name="microscope-setup-emulated.png" path="microscope-setup-emulated.png" size="15155" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temextreg window" date="1206389445" name="j1230-temextreg.png" path="j1230-temextreg.png" size="11424" user="Main.BillRice" version=""
Added:
>
>
META FILEATTACHMENT attachment="jeol_1230_computer.pdf" attr="" comment="serial port command instructions for jeol 1230" date="1206396439" name="jeol_1230_computer.pdf" path="jeol_1230_computer.pdf" size="15093571" stream="jeol_1230_computer.pdf" user="Main.BillRice" version="0"
 

Revision 1124 Mar 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows
    j1230-temextreg.png
  • Settings in TemServer? 20xx (visible when viewing Properties) are :
    j1230-temserver20xx.png

Digital Micrograph communication with microscope

  • Digital Micrograph communicates with J1230 through serial port by default
Changed:
<
<
  • Setup is as follows:
  • When emulator is running, can optionally use JEOL COM as microscope rather than JEOL 12n0
  • In either option, there is a test panel for testing Digital Micrograph's ability to control microscope
>
>
  • Setup is as follows:
    microscope-setup-normal.png
  • When emulator is running, can optionally use JEOL COM as microscope rather than JEOL 12n0
Added:
>
>		 microscope-setup-emulated.png
  • In either option, there is a test panel for testing Digital Micrograph's ability to control microscope
    microscope-setup-test.png
 
Added:
>
>
 

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL? python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60

Leginon Installation

  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension? 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box

  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

Changed:
<
<		 * dm-normal communication:
microscope-setup-normal.png
>
>

 
Changed:
<
<		 * dm - emulated communication:
>
>
Deleted:
<
<		 microscope-setup-emulated.png
 
Deleted:
<
<		 * dm-test panel:
microscope-setup-test.png
 
META FILEATTACHMENT attr="" autoattached="1" comment="dm-normal communication" date="1206394754" name="microscope-setup-normal.png" path="microscope-setup-normal.png" size="14580" user="Main.BillRice" version=""
Added:
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="dm-test panel" date="1206394808" name="microscope-setup-test.png" path="microscope-setup-test.png" size="32840" user="Main.BillRice" version=""
 
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="dm - emulated communication" date="1206394786" name="microscope-setup-emulated.png" path="microscope-setup-emulated.png" size="15155" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temextreg window" date="1206389445" name="j1230-temextreg.png" path="j1230-temextreg.png" size="11424" user="Main.BillRice" version=""
Deleted:
<
<
META FILEATTACHMENT attachment="microscope-setup-test.png" attr="" comment="dm-test panel" date="1206394807" name="microscope-setup-test.png" path="microscope-setup-test.png" size="32840" stream="microscope-setup-test.png" user="Main.BillRice" version="0"
 

Revision 1024 Mar 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows
    j1230-temextreg.png
  • Settings in TemServer? 20xx (visible when viewing Properties) are :
    j1230-temserver20xx.png

Digital Micrograph communication with microscope

  • Digital Micrograph communicates with J1230 through serial port by default
  • Setup is as follows:
  • When emulator is running, can optionally use JEOL COM as microscope rather than JEOL 12n0
  • In either option, there is a test panel for testing Digital Micrograph's ability to control microscope

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL? python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60

Leginon Installation

  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension? 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box

  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

* dm-normal communication:
microscope-setup-normal.png

* dm - emulated communication:
microscope-setup-emulated.png

Added:
>
>		 * dm-test panel:
microscope-setup-test.png
 
META FILEATTACHMENT attr="" autoattached="1" comment="dm-normal communication" date="1206394754" name="microscope-setup-normal.png" path="microscope-setup-normal.png" size="14580" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" user="Main.BillRice" version=""
Added:
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="dm - emulated communication" date="1206394786" name="microscope-setup-emulated.png" path="microscope-setup-emulated.png" size="15155" user="Main.BillRice" version=""
 
META FILEATTACHMENT attr="" autoattached="1" comment="temextreg window" date="1206389445" name="j1230-temextreg.png" path="j1230-temextreg.png" size="11424" user="Main.BillRice" version=""
Changed:
<
<
META FILEATTACHMENT attachment="microscope-setup-emulated.png" attr="" comment="dm - emulated communication" date="1206394786" name="microscope-setup-emulated.png" path="microscope-setup-emulated.png" size="15155" stream="microscope-setup-emulated.png" user="Main.BillRice" version="0"
>
>
META FILEATTACHMENT attachment="microscope-setup-test.png" attr="" comment="dm-test panel" date="1206394807" name="microscope-setup-test.png" path="microscope-setup-test.png" size="32840" stream="microscope-setup-test.png" user="Main.BillRice" version="0"
 

Revision 924 Mar 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows
    j1230-temextreg.png
  • Settings in TemServer? 20xx (visible when viewing Properties) are :
    j1230-temserver20xx.png

Digital Micrograph communication with microscope

  • Digital Micrograph communicates with J1230 through serial port by default
  • Setup is as follows:
  • When emulator is running, can optionally use JEOL COM as microscope rather than JEOL 12n0
  • In either option, there is a test panel for testing Digital Micrograph's ability to control microscope

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL? python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60

Leginon Installation

  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension? 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box

  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

* dm-normal communication:
microscope-setup-normal.png

Added:
>
>		 * dm - emulated communication:
microscope-setup-emulated.png

META FILEATTACHMENT attr="" autoattached="1" comment="dm-normal communication" date="1206394754" name="microscope-setup-normal.png" path="microscope-setup-normal.png" size="14580" user="Main.BillRice" version=""
 
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temextreg window" date="1206389445" name="j1230-temextreg.png" path="j1230-temextreg.png" size="11424" user="Main.BillRice" version=""
Changed:
<
<
META FILEATTACHMENT attachment="microscope-setup-normal.png" attr="" comment="dm-normal communication" date="1206394754" name="microscope-setup-normal.png" path="microscope-setup-normal.png" size="14580" stream="microscope-setup-normal.png" user="Main.BillRice" version="0"
>
>
META FILEATTACHMENT attachment="microscope-setup-emulated.png" attr="" comment="dm - emulated communication" date="1206394786" name="microscope-setup-emulated.png" path="microscope-setup-emulated.png" size="15155" stream="microscope-setup-emulated.png" user="Main.BillRice" version="0"
 

Revision 824 Mar 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows
    j1230-temextreg.png
  • Settings in TemServer? 20xx (visible when viewing Properties) are :
    j1230-temserver20xx.png

Digital Micrograph communication with microscope

  • Digital Micrograph communicates with J1230 through serial port by default
  • Setup is as follows:
  • When emulator is running, can optionally use JEOL COM as microscope rather than JEOL 12n0
  • In either option, there is a test panel for testing Digital Micrograph's ability to control microscope

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL? python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60

Leginon Installation

  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension? 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box

  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

Added:
>
>		 * dm-normal communication:
microscope-setup-normal.png
 
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temextreg window" date="1206389445" name="j1230-temextreg.png" path="j1230-temextreg.png" size="11424" user="Main.BillRice" version=""
Added:
>
>
META FILEATTACHMENT attachment="microscope-setup-normal.png" attr="" comment="dm-normal communication" date="1206394754" name="microscope-setup-normal.png" path="microscope-setup-normal.png" size="14580" stream="microscope-setup-normal.png" user="Main.BillRice" version="0"
 

Revision 724 Mar 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows
    j1230-temextreg.png
  • Settings in TemServer? 20xx (visible when viewing Properties) are :
    j1230-temserver20xx.png
Added:
>
>

Digital Micrograph communication with microscope

  • Digital Micrograph communicates with J1230 through serial port by default
  • Setup is as follows:
  • When emulator is running, can optionally use JEOL COM as microscope rather than JEOL 12n0
  • In either option, there is a test panel for testing Digital Micrograph's ability to control microscope
 

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL? python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60

Leginon Installation

  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension? 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box

  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temextreg window" date="1206389445" name="j1230-temextreg.png" path="j1230-temextreg.png" size="11424" user="Main.BillRice" version=""

Revision 624 Mar 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
Changed:
<
<
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows
>
>
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows
Added:
>
>		 j1230-temextreg.png
  • Settings in TemServer? 20xx (visible when viewing Properties) are :
    j1230-temserver20xx.png
 

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL? python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60
Changed:
<
<		 ---++++ Leginon Installation
>
>

Leginon Installation

 
  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension? 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box

  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

Deleted:
<
<		 * temextreg window:
j1230-temextreg.png
 
Deleted:
<
<		 * temserver20xx settings:
j1230-temserver20xx.png
 
Changed:
<
<
META FILEATTACHMENT attachment="j1230-temextreg.png" attr="" comment="temextreg window" date="1206389445" name="j1230-temextreg.png" path="j1230-temextreg.png" size="11424" stream="j1230-temextreg.png" user="Main.BillRice" version="0"
META FILEATTACHMENT attachment="j1230-temserver20xx.png" attr="" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" stream="j1230-temserver20xx.png" user="Main.BillRice" version="0"
>
>
Added:
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="temextreg window" date="1206389445" name="j1230-temextreg.png" path="j1230-temextreg.png" size="11424" user="Main.BillRice" version=""
 

Revision 524 Mar 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL? python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60 ---++++ Leginon Installation
  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension? 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box

  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007 * temextreg window:
j1230-temextreg.png

Added:
>
>		 * temserver20xx settings:
j1230-temserver20xx.png
 
META FILEATTACHMENT attachment="j1230-temextreg.png" attr="" comment="temextreg window" date="1206389445" name="j1230-temextreg.png" path="j1230-temextreg.png" size="11424" stream="j1230-temextreg.png" user="Main.BillRice" version="0"
Added:
>
>
META FILEATTACHMENT attachment="j1230-temserver20xx.png" attr="" comment="temserver20xx settings" date="1206389539" name="j1230-temserver20xx.png" path="j1230-temserver20xx.png" size="13578" stream="j1230-temserver20xx.png" user="Main.BillRice" version="0"
 

Revision 424 Mar 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL? python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60 ---++++ Leginon Installation
  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension? 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box

  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

Added:
>
>		 * temextreg window:
j1230-temextreg.png

META FILEATTACHMENT attachment="j1230-temextreg.png" attr="" comment="temextreg window" date="1206389445" name="j1230-temextreg.png" path="j1230-temextreg.png" size="11424" stream="j1230-temextreg.png" user="Main.BillRice" version="0"
 

Revision 324 Mar 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Automated Control and Robotics on 1230

Changed:
<
<
  • Currently have SerialEM installed and running on J1230
  • SerialEM needs to have Te
>
>
  • Options for Automated Control
    • SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
Added:
>
>
    • AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
    • Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
    • home - written software

Microscope Communication with PC

  • Currently connected through both COM1 (serial) and ethernet
  • Digital Micrograph currently using COM1
  • Have TemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
  • Settings required for TemServer20xx are in TemExtReg.exe program, as follows
 

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL? python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60 ---++++ Leginon Installation
  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension? 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box

  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

Revision 224 Mar 2008 - Main.BillRice

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

Gatlan Gun information

Sublevel topic

subsub level topic

>
>

Automated Control and Robotics on 1230

  • Currently have SerialEM installed and running on J1230
  • SerialEM needs to have Te
Added:
>
>

Leginon

Installation

Pre-Requisites

  • Downloaded Leginon-prereq-wininstall.zip from James Pulokas
    • install Python 2.52
    • install pywin32 (may need MFC71.dll on some PC's; was already installed on 1230)
    • install wxpython
    • install MySQL? python client
    • install PIL, the Python Imaging Library
    • install numpy 1.04
    • install scipy 0.60 ---++++ Leginon Installation
  • Will be using version 1.5 of Leginon
  • TO BE DONE:
    • Install NumExtension? 1.1.0
    • Install pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
    • Install sinedon -r39
    • Install pyami - r69
    • Install Imageviewer
    • Install Leginon - r5457
    • Edit default.cfg to configure Leginon to communicate with proper database
    • Edit sinedon.cfg configure Leginon to communicate with proper database
    • Set up database and web server on outside linux box
 
  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

Revision 119 Oct 2007 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Gatlan Gun information

Sublevel topic

subsub level topic

  • Set ALLOWTOPICVIEW =

-- BillRice - 19 Oct 2007

View topic  |  History: r26 < r25 < r24 < r23  |  More topic actions...
 
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