Diamond Remote Tomo5, Operation Manual

Page: 3 / 29

Document Title:
Remote Tomo5 operation guide for eBIC microscopes
Author(s):
Kyle Morris
Julika Radecke
Andrew Howe Version:
2.0.3
Date:
27 Jun 2022
If you have any questions at any point during set-up, please ask your Local Contact for assistance Page 3 of 29
Contents
Contents ............................................................................................................................................ 3
1 Preparation ................................................................................................................................ 4
1.1 Communication .................................................................................................................. 4
1.2 Remote connection ........................................................................................................... 4
1.3 Quick start guide ............................................................................................................... 4
1.4 Reasonable session timings ............................................................................................ 4
2 User interface summaries ........................................................................................................ 5
3 Microscope setup and screening ........................................................................................... 8
3.1 Grid loading, Atlas and Presets ....................................................................................... 8
3.1.1 Initial checks and start up .......................................................................................................................... 8
3.1.2 Collect your Atlas ....................................................................................................................................... 8
3.1.3 Inspect your Atlas..................................................................................................................................... 10
3.1.4 Check your imaging condition Presets .................................................................................................... 10
3.1.5 Dose calculation ....................................................................................................................................... 12
3.2 Image Shift Calibrations ................................................................................................. 13
3.2.1 Prepare for image shift calibrations ......................................................................................................... 13
3.2.2 Find eucentric height ................................................................................................................................ 13
3.2.2.1 Automatic eucentric height troubleshooting _________________________________________ 13
3.2.2.2 Image Filter Settings troubleshooting ______________________________________________ 14
3.2.2.3 Manual eucentric height troubleshooting ___________________________________________ 14
3.2.3 Target a feature for Image Shift calibrations............................................................................................ 15
3.2.4 Calibrate the Image Shifts ........................................................................................................................ 16
4 Tomography setup .................................................................................................................. 17
4.1 Setup ................................................................................................................................. 17
4.1.1 Session setup ........................................................................................................................................... 17
4.1.2 Identify tomography targets ..................................................................................................................... 18
4.1.2.1 Overview (identify square or lamella) ______________________________________________ 18
4.1.2.2 Lamella tilt correction (if applicable) _______________________________________________ 18
4.1.2.3 Search Maps
– medium mag montaging (identify hole or cellular targets)__________________ 19
4.1.3 Acquisition setup ...................................................................................................................................... 20
4.1.3.1 Set up batch position ___________________________________________________________ 20
4.1.3.2 Validate batch position _________________________________________________________ 22
4.1.3.3 Add batch position _____________________________________________________________ 22
4.1.4 Eucentric height refinement strategy ....................................................................................................... 23
4.1.4.1 Refine target positions__________________________________________________________ 23
5 Final checks and data collection .......................................................................................... 24
5.1 Auto Functions and alignment ...................................................................................... 24
5.1.1 Alignments via Autofunctions ................................................................................................................... 24
5.1.2 Beam centring .......................................................................................................................................... 25
5.1.1 Objective aperture .................................................................................................................................... 25
5.1.2 Zero-loss peak ......................................................................................................................................... 25
5.2 Start automated acquisition ........................................................................................... 26
5.2.1 Check your tomography acquisition parameters ..................................................................................... 26
5.2.2 Start tomography acquisition ................................................................................................................... 27
5.2.3 Plan to request your dewar return ........................................................................................................... 27
5.2.4 Monitor your data collection ..................................................................................................................... 28
5.2.5 Final steps ................................................................................................................................................ 29