BakingTray
  • BakingTray Documentation
  • Getting Started
    • Hardware requirements
    • Known issues
    • Initial Installation
      • Software installation
      • Setting up ScanImage
    • Hardware setup
      • Motor Setup
        • PI stage setup
        • Calibrating a linear actuator
        • Verifying stage motions
      • Setting up a VT1000 vibratome
      • Setting up the laser
    • Finishing the install
      • Check the noise on your amplifiers
      • Starting BakingTray
      • Settings Files
      • Calibration
        • Basic calibrating procedures
        • Calibrating image size
        • Achieving high stitching accuracy
        • Fine-tuning positioning accuracy
        • Stitching tweak walkthrough
    • Stitching data
  • Users
    • Introduction
    • Sample preparation
    • User Guide
      • Starting BakingTray
      • Step 0: Loading the sample
      • 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
    • Choosing imaging settings
    • Troubleshooting
      • Hardware problems
      • Computer problems
      • Cutting problems
      • Imaging problems
    • Data structure
    • autoROI
  • Developers
    • Developers
      • Code overview
      • Developer notes
      • Motion control classes
      • The recipe file
      • Auto-ROI
      • Simulated mode
      • Contributing
    • FAQ
    • Gallery
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  2. User Guide

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. You only need to do another preview scan in exceptional circumstances (see below).

Do not re-load the recipe after you have asked to resume. This will revert important settings to default values.

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, or because somehow how the sample vanished, etc, 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. 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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Last updated 2 years ago