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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  1. Getting Started

Known issues

PreviousHardware requirementsNextInitial Installation

Last updated 6 months ago

In general BakingTray is very stable and almost all acquisitions complete without errors. The full list of issue can be found on the . The more notable issues are as follows:

  • During acquisition with linear scanners or a high level of averaging with resonant scanners there are multiple instances of duplicate tiles appearing in the preview window. This does not affect the saved data.

  • We use an to control the PMT gains. This works but we see the following bug: there is a rare chance that, when BakingTray is open, . We work around this by disabling PMT auto-on and having BakingTray issue the PMT off command at the conclusion of acquisition only. We experience no problems or acquisition failures when working like this.

Hardware-related issues.

  • PROBLEM: Coherent lasers rarely switch off or close the shutter during the first section. This has never happened later in the acquisition. SOLUTION: Deleting the files in the acquisition directory and re-starting the acquisition.

BakingTray issue tracker
Issue #20
Issue #234
NI USB-6343
switching off the PMTs causes MATLAB to crash