Difference: GatlingGun (25 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"
View topic  |  History: r26 < r25 < r24 < r23  |  More topic actions...
 
Copyright © by the contributing authors. All material on this collaboration platform is the property of the contributing authors.
Ideas, requests, problems regarding this intranet, Send feedback