BakingTray
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BakingTray Documentation
Getting Started
Hardware requirements
Known Issues
Installation
Stitching data
Users
Introduction
Sample preparation
User Guide
Starting BakingTray
Step 1: Setting imaging parameters
Step 2: Preparing the sample
Step 3: Selecting the imaging area
Step 4: Starting the acquisition
Step 5: Concluding the acquisition
Setting up checklist
Resuming an acquisition
Manual ROI acquisitions
Excitation choices
Selecting a resolution
Problems and solutions
Data structure
Legacy User Guide
autoROI
Imaging multiple brains at once
Developers
Developers
FAQ
Gallery
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Resuming an acquisition

Restarting a stopped acquisition

It is possible to resume an acquisition that stopped for whatever reason. The following steps can be performed even if MATLAB crashed or the acquisition was interrupted by a power cut.
Perform the following steps to resume an acquisition:
  • Select Sample > Resume Acquisition from the BakingTray menu. Load the recipe file from the acquisition directory containing the sample you wish to resume.
  • You will be asked to confirm whether you wish to resume the acquisition.
  • Press "Yes" and double-check the parameters in the recipe and prepare GUI.
  • You will then be presented with a new GUI asking how the acquisition should be resumed. e.g. if the last section was partially completed, should the existing data be discarded and the section re-imaged.
  • You are responsible for turning the PMTs back on. Similarly for ensuring the laser is on and the shutter is open.
  • The Acquisition GUI will now appear. Press "Bake" to start the acquisition. Repeating the preview and autothresh is not normally necessary.

Notes

  • It is not necessary to do another preview scan and repeat the auto-thresh under most circumstances. If you are re-starting the acquisition because of an issue related with the auto-ROI, then of course you should do another preview and another Auto-Thresh before pressing Bake.
  • If you have reason to think the sample surface might have moved (e.g. there is a long delay before you resume or you have changed the blade) then you might want to take a preview scan first and repeat the auto-thresh. Then watch how it cuts and tweak objective height.
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Setting up checklist
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Manual ROI acquisitions
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