JEOLCOM installation specifics » History » Version 17
Anchi Cheng, 04/04/2015 12:33 AM
1 | 1 | Anchi Cheng | h1. JEOL installation specifics |
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3 | 2 | Anchi Cheng | These implementations have pyscope modules included in our repository |
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5 | 1 | Anchi Cheng | h2. JEOL 1230 |
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7 | Developed at New York Structure Biology Center |
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8 | 2 | Anchi Cheng | |
9 | Please contact David Stokes |
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11 | 3 | Anchi Cheng | h2. JEOL 1400 and 3200 (and other scopes with JEOL's COM library) |
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13 | 13 | Anchi Cheng | Developed originally at Northwestern University by Christian Suloway |
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15 | 10 | Anchi Cheng | h3. Install 32-bit version of myami package on the associated camera computer |
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17 | 12 | Anchi Cheng | * Instead of installing myami package on JEOL scope-controlling PC, the access to JEOLCOM usually work through the computer controlling the digital camera, regardless of the camera manufacturer. |
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19 | 1 | Anchi Cheng | * In addition, probably because of the way JEOLCOM works, the installation is limited to 32-bit version. |
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21 | h3. Alternatively, install myami package on JEOL scope-controlling microscope |
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23 | * This is only possible if this PC has TEMExternal3 installed and if it is on the same secured network as Leginon processing and database server. |
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25 | See [[JEOL External3 setup]] |
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27 | 7 | Anchi Cheng | {{include(comtypes installer)}} |
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29 | 1 | Anchi Cheng | Please check [[Windows_Installation_All]] for important installation instruction regarding comtypes |
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31 | 9 | Anchi Cheng | Notes from the developer: |
32 | 6 | Anchi Cheng | <pre> |
33 | There are a few conversion factor at the top of the file that may need adjustment depending on the microscope. |
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34 | 1 | Anchi Cheng | </pre> |
35 | 13 | Anchi Cheng | |
36 | h2. jeol.cfg |
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38 | jeol.cfg records some instrument specific parameters that are required to convert the COM output to SI units that Leginon depends on as well as standard focus values needed for initializing defocus reference. |
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40 | See [[Setup and Calibration for jeol.cfg]] |
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41 | 4 | Anchi Cheng | |
42 | h2. instruments.cfg |
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44 | [scope] |
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45 | class: jeolcom.Jeol |
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46 | cs: 4.1e-3 |
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48 | h2. Testing with pyscope |
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50 | In python command |
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51 | <pre> |
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52 | 15 | Neil Voss | from pyscope import jeolcom |
53 | 4 | Anchi Cheng | t =jeolcom.Jeol() |
54 | t.getMagnification() |
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55 | </pre> |
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56 | 5 | Anchi Cheng | |
57 | You should get the current magnification at the microscope when the main viewing screen is up |
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58 | 14 | Anchi Cheng | |
59 | h2. Leginon Calibration specifics |
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61 | 16 | Anchi Cheng | JEM scopes do not have a high level function we can access through scripting to move image shift without affecting beam location. Therefore, any Leginon node that uses IMAGE SHIFT move type should be changed to BEAM-IMAGE SHIFT. |
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63 | This affects calibration procedure in two ways: |
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64 | * Beam Shift should be calibrated at mid and high mags (i.e. mags for hl and fa,fc,en,ef) |
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65 | 14 | Anchi Cheng | * Image Shift should be calibrated at smaller shift distance if the beam moves too much to affect correlation. |
66 | 17 | Anchi Cheng | |
67 | h2. [[Leginon Operation for JEM scopes]] |