Continuous tilt electron diffraction recording » History » Version 28
Anchi Cheng, 11/13/2020 01:29 PM
1 | 6 | Anchi Cheng | h1. Continuous tilt electron diffraction recording use Ceta or Ceta-D camera and TFS scopes |
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3 | 22 | Anchi Cheng | Micro-ED involves recording 3D crystal electron diffraction pattern during a continuous stage tilt. Leginon implementation of this application includes the listed components below and is available by using myami-beta branch until it is officially added to future release. As is, it is only fully implemented for TFS Ceta or Ceta-D camera. |
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5 | Since many of the feature required here are not available through Standard or Advanced TEM Scripting from TFS, AutoIt scripts are used in several places. |
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7 | h2. Components of the feature |
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9 | 5 | Anchi Cheng | # Diffraction mode TEM instrument |
10 | 8 | Anchi Cheng | # Beamstop control: achieved by AutoIt Scripts BeamstopIn and BeamstopOut |
11 | 9 | Anchi Cheng | # Rolling-shutter movie acquisition using TIA interface |
12 | 23 | Anchi Cheng | # [[TIA raw data conversion|Data conversion]] and upload of the movies into Leginon database and crystallography format |
13 | 4 | Anchi Cheng | # [[ MSI-Diffr application ]] |
14 | 11 | Anchi Cheng | # [[Camera length calibration]] |
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16 | h2. Installation (assuming that you've already have Leginon installation). |
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18 | # Check that you have access to Advanced TEM Scripting (frame-saving upgrade not needed). |
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19 | 28 | Anchi Cheng | # Install or set environment to use git branch myami-3.5 and up or the current myami-beta on TFS microscope with Ceta camera as well as your leginon linux box and webserver for myamiweb. |
20 | 10 | Anchi Cheng | # import updated Calibrations application (see [[Steps_involved_in_the_installation]]) |
21 | # import MSI-diffraction and settings from your_myami/leginon/applications (see general description of [[Steps_involved_in_the_installation]] regarding importing application and additional settings for the application) |
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22 | 5 | Anchi Cheng | # [[Setup Diffraction mode TEM instrument]] |
23 | 7 | Anchi Cheng | # [[Setup Ceta to use Advanced TEM Scripting]] |
24 | 3 | Anchi Cheng | # [[AutoIt program and script compilation]] |
25 | 20 | Anchi Cheng | # [[Setup movie upload with diffrtransfer.py]] |
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27 | 27 | Anchi Cheng | h2. Microscope optical settings |
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29 | 27 | Anchi Cheng | * Gun Lens: 7.1 is the typical we use. This delievers about 1/4 of the beam intensity of Gun Lens 3.3 on Glacios |
30 | * C2 Aperture: 20 um for any SA and diffraction presets. 150 um, or what you typically use that does not block the beam for grid atlas |
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31 | * Probe mode: nano probe parallel illumination whereever possible |
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33 | h2. Presets unique for this application (Glacios with CetaD and 0.9 Å resolution) |
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35 | |preset name|TEM|magnification(camera length)|SpotSize|Parallel?|Notes| |
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36 | |hl|Glacios|8500|10|No|Minimize exposure dose is important since this preset is used for all target tracking and eucentric height adjustment| |
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37 | |df|DiffrGlacios|1100|10|Yes|Exposure time is only relevant for Diffraction node where single acquistion is taken| |
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39 | 26 | Anchi Cheng | h2. Calibration |
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41 | 1 | Anchi Cheng | # [[Camera length calibration]] |
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43 | h2. Usage |
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45 | h3. Check these before you start: |
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47 | 27 | Anchi Cheng | # Set gun lens value. This must be done manually. Use "Free control" option if needed. |
48 | # Confirm that instruments.cfg is properly set up to use feicam for Ceta camera. Especially if you use Falcon camera on the same instrument for imaging. |
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49 | # Open TUI. Select and insert BM-Ceta in the camera tab. Confirm that tui_acquire.au3 validation items are set [[Autoit program and script compilation#TUIAcquire-Testing|correctly]]. |
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50 | # Make sure TIA window is available and the Export Series shortcut is shown as required by [[Autoit program and script compilation#TiaExportSeries-Testing|TiaExportSeries.au3]] |
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52 | 13 | Anchi Cheng | h3. Start MSI-DIffr application and assign client as required. |
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54 | 1 | Anchi Cheng | h3. [[Setup df preset]] |
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56 | h3. Grid atlas collection |
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58 | 1. Select gr preset to scope, with flucam showing the grid and aperture, draw on the computer screen the location of the centerred small C2 aperture. |
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59 | 2. Select a larger C2 aperture for grid atlas collection. |
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60 | 3. collect grid atlas. |
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61 | 4. Reselect the small C2 aperture. Make sure it is still centered. |
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63 | h3. Queue up potential crystals |
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65 | 1. Pick square and then pick "hole" for intermediate mag image of potential crystals. (This is no different from any other MSI application). |
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66 | 2. Submit preview targets in "DExposure Targeting" node for a small rotation image and confirm whether it diffracts or not. |
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67 | 3. Submit the good crystal positions as acquisition targets into the queue in "DExposure Targeting" node. No focus target is needed. |
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68 | 4. If needed, modify "DExposure" settings for start, range, and speed of the tilt. |
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69 | 5. Click "process queue" tool to start collection |
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71 | h3. Diffraction series naming convension |
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73 | The diffraction series is named after the parent image database id and target number in its target list. For example, 123456_1 |