Related Manuals for Diamond Remote Tomo5
Summary of Contents for Diamond Remote Tomo5
- Page 1 Remote Tomo5 operation guide for eBIC microscopes Revision: 2.0.3 Revision date: 27 Jun 2022 Author(s): Kyle Morris Julika Radecke Andrew Howe...
- Page 2 The level of detail is targeted at a standard eBIC operator. The user is ultimately responsible for their use of eBIC and Diamond systems. If you are in doubt about an action you need to perform or are unable to progress, then please reach out to the eBIC Local Contact assigned to your session for assistance.
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Page 3: Table Of Contents
Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 Contents Contents ............................3 Preparation ..........................4 Communication ........................4 Remote connection ......................4 Quick start guide ....................... 4 Reasonable session timings .................... -
Page 4: Preparation
Remote access and analysis guide. You will not see an instrument until your session is scheduled but you should check you can successfully log in to nx-cloud.diamond.ac.uk via NoMachine. 1.3 Quick start guide 1) Make your Atlas session 2) Atlas your grids... -
Page 5: User Interface Summaries
Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 2 User interface summaries Team Viewer To switch between the virtual monitor hosting the TEM user interface and TFS Tomo, use the Team Viewer Monitor buttons. - Page 6 Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 TEM User Interface (TUI) – user interface It is in general becoming less necessary to use TUI but for some operations later in the guide you will need to access this interface.
- Page 7 Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 Thermo Fisher Scientific Tomo software – user interface You can generally understand navigation through the tomography workflow via working left to right through the ‘Workflow tabs’, and top to bottom through the ‘Workflow tasks’...
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Page 8: Microscope Setup And Screening
Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 3 Microscope setup and screening 3.1 Grid loading, Atlas and Presets 3.1.1 Initial checks and start up Your Local Contact will have loaded and inventoried the autoloader cassette... - Page 9 Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 Atlas collection: Collect an Atlas of the chosen grid(s) Atlas > Screening Select the checkbox of each grid you want to acquire an Atlas of and select Close Col Valves If acquiring more than one Atlas, go to autoloader and switch the turbo to “Always On”.
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Page 10: Inspect Your Atlas
Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 3.1.3 Inspect your Atlas Inspect your single or multiple Atlases for targets by clicking on the grid in the left panel Left-click drag to move around, middle scroll to zoom in-out When you have chosen your grid for target setup, select it and click ‘Load Sample’... - Page 11 Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 Take a Preview using the Search Preset Search is used in the Tomography tab to setup positions. Make sure the magnification is adequate to show your feature of interest and to fit both the Exposure and the Tracking/Focus area in the field of view.
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Page 12: Dose Calculation
Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 3.1.5 Dose calculation Your LC will have told you the physical pixel dose rate over vacuum. Follow the example calculation below to calculate and enter your target exposure time based on your desired target dose per tilt or in total (e /Å... -
Page 13: Image Shift Calibrations
Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 3.2 Image Shift Calibrations 3.2.1 Prepare for image shift calibrations Continue to use the Atlas > Screening tab to navigate your loaded grid... -
Page 14: Image Filter Settings Troubleshooting
Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 defocus offset (-25 to -50 µm) and/or a shorter exposure time to decrease cross- correlation from hole patterns. -
Page 15: Target A Feature For Image Shift Calibrations
Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 If Tomo still fails to automatically find eucentric height, you can use manual eucentric height calibration: Centre over a reasonably large ice crystal in Overview mag in the Tomo preparation tab, then switch to the ‘Set’... -
Page 16: Calibrate The Image Shifts
Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 If you found the feature remained centred during targeting, then you may choose to skip image shift calibrations If you needed to recentre the feature during targeting, you should calibrate the Image Shifts. -
Page 17: Tomography Setup
Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 4 Tomography setup 4.1 Setup 4.1.1 Session setup Tomography > New session > Session setup Naming convention: Supervisor_YYYYMMDD_XXXXXX_visit-ID_autoloader-#_Tomo... -
Page 18: Identify Tomography Targets
Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 4.1.2 Identify tomography targets 4.1.2.1 Overview (identify square or lamella) Move to a square of interest Tomography tab > Batch position Click on the tab for Atlas Navigate to a region of interest with Right click >... -
Page 19: Search Maps - Medium Mag Montaging (Identify Hole Or Cellular Targets)
Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 Tilt the stage to 2X the known milling angle using a positive tilt, by using ‘Set Tilt (°)’ and ‘Set’... -
Page 20: Acquisition Setup
Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 Inspect Overview or Search Map: move to a region of interest and take Search image Right click > Move Stage Here > Acquire Search Inspect Search image, move stage to target and setup collection (described below) Reposition if required: Right click →... - Page 21 Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 Ensure the tracking/focus area is (mostly) on carbon with tracking features; avoid cracks, ice contamination or overly thick regions.
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Page 22: Validate Batch Position
Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 4.1.3.2 Validate batch position Tilt the stage using ‘Set Tilt (°)’ to check tilted acquisition will be successful on the batch areas Be aware of what is close and what is going to come into the beam. -
Page 23: Eucentric Height Refinement Strategy
Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 4.1.4 Eucentric height refinement strategy To check the eucentric height is properly calibrated for your batch positions, there are a number of available strategies. -
Page 24: Final Checks And Data Collection
Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 5 Final checks and data collection 5.1 Auto Functions and alignment 5.1.1 Alignments via Autofunctions Navigate in the Atlas (refer to 3.1.3) to an area of carbon to perform alignments You must be at eucentric height (refer to 3.2.2) and the objective aperture should be removed... -
Page 25: Beam Centring
Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 5.1.2 Beam centring Switch to the TEM user interface (TUI) Insert the flu screen Load the TEM Control Pads Simulator... -
Page 26: Start Automated Acquisition
Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 5.2 Start automated acquisition 5.2.1 Check your tomography acquisition parameters You should refer to your dose calibration in 3.1.5 to double check those collection parameters for your Exposure Preset are reasonable. -
Page 27: Start Tomography Acquisition
Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 5.2.2 Start tomography acquisition Double check data collection parameters agree with dose calculation and desired tilt scheme, then begin acquisition Tomography →... -
Page 28: Monitor Your Data Collection
Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 5.2.4 Monitor your data collection your responsibility monitor your data collection. Please refer ‘Data_access_and_analysis_guide’ for how to do this. -
Page 29: Final Steps
Document Title: Author(s): Version: Remote Tomo5 operation guide for eBIC microscopes Kyle Morris 2.0.3 Julika Radecke Date: Andrew Howe 27 Jun 2022 5.2.5 Final steps Click on (1) the highlighted cross to close TeamViewer (Take care that you do not accidentally close the “TEM User Interface”)