Falcon Orius combo installation and setup » History » Version 11
Anchi Cheng, 02/02/2016 02:34 PM
1 | 1 | Anchi Cheng | h1. Falcon Orius combo installation and setup |
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3 | h1. Falcon/Orius combo unique installation and setup |
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5 | h2. Falcon/Orius is controlled by the same computer as the microscope |
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7 | Currently working configuration uses TIA and TIA Scripting to control Falcon and Gatan Digital Micrograph Scripting to control Orius. |
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9 | h2. Extra Package and Installation |
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11 | * Use all 32-bit version of Windows installer |
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12 | |_.program/package|_.notes| |
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13 | 5 | Anchi Cheng | |TecnaiCCD.dll | For Orius to be controlled through DM. Should come with the microscope | |
14 | 6 | Anchi Cheng | |Tia.dll | For Falcon to be controlled through ESVision(TIA). Should come with the microscope | |
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16 | {{include(comtypes installer)}} |
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18 | h3. Register TecnaiCCD.dll (It may have been registered already) |
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20 | * From the command prompt, run the following commands. You may need to enter the full path of the dll: |
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21 | <pre>REGSVR32 TecnaiCCD.dll</pre> |
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23 | 9 | Anchi Cheng | h3. Run checkcom.py |
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25 | * From a command line window: |
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26 | <pre>cd C:\python27\Lib\site-packages\pyscope |
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27 | 8 | Anchi Cheng | C:\python27\python.exe checkcom.py</pre> |
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29 | * The output sould contain this output for DM scripting |
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30 | <pre> |
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31 | 8 | Anchi Cheng | Found COM typelib named: TecnaiCCD. |
32 | 1 | Anchi Cheng | </pre> |
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34 | and one of these outputs for TIA scripting |
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35 | <pre> |
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36 | 8 | Anchi Cheng | Found COM typelib named: ESVision.Application done. |
37 | 1 | Anchi Cheng | </pre> |
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39 | h2. instruments.cfg |
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41 | {{include(Instrumentscfg_for_falcon_orius)}} |
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43 | h2. Setup |
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45 | * Set camera configuration to give the [[Leginon Image Orientation|standard Leginon orientation]]. For example, we need 270 degree rotation and flip around the vertical axis on FEI F20. Note that the rotation required is different if it is installed post-GIF and/or on Krios. |
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46 | * Set the [[Low_dose_shutter_configuration_for_Gatan_camera_in_Digital_Micrograph_program|shutter configuration in DM]] to protect the specimen when camera is not taking images. |
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47 | * Create the folder to store the dose fractionation raw frames. Frames are saved as unsigned 16-bit mrc image stack in K2 computer under D:\frames by default as set in the code inside pyscope/dmsem.py in the function calculateFileSavingParams. You must create the frames directory first. Leginon will not do that for you. You may change where the frames are saved here but will need to make corresponding changes when setting up [[DDD_raw_frame_file_transfer|raw frame file transfer]] |
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48 | * Setup [[DDD_raw_frame_file_transfer|raw frame file transfer]] from a network data server. |
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49 | * Unless you want to develop your own frame alignment program. We recommend that you [[appion:Direct_Detector_Frame_Processing|use Appion to do frame gain correction and alignment]]. These are parallelized by images so it cam almost keep up with the acquisition. |
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51 | h2. Testing with pyscope |
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53 | 3 | Anchi Cheng | Type these commands in python IDLE if you want to see the error message. |
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55 | 1 | Anchi Cheng | h3. Testing Orius |
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57 | <pre> |
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58 | 10 | Anchi Cheng | from pyscope import gatan |
59 | 1 | Anchi Cheng | g = gatan.Gatan() |
60 | g.setExposureTime(100) |
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61 | g.getImage() |
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62 | </pre> |
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64 | h3. Testing Falcon |
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66 | <pre> |
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67 | from pyscope import tia |
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68 | g = tia.TIA_Falcon() |
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69 | g.setExposureTime(1000) |
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70 | g.getImage() |
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71 | </pre> |
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73 | 11 | Anchi Cheng | {{include(pyscope_test_result array)}} |
74 | 1 | Anchi Cheng | h2. Programs to open before Leginon Client: Digital Micrograph and then TIA |