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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Data structure

PreviousImaging problemsNextautoROI

Last updated 4 years ago

A single sample directory contains one sample (one imaging session). Within this you will find the following files:

This directory contains:

  • recipe_XXX.yml -- This text file is and contains the parameters the user entered to set up the acquisition. It also contains extra information generated by BakingTray, such as the scanning parameters. This file is required for the individual images to be assembled (stitched) into full planes.

  • acqLog_XXX.txt -- Logs major acquisition events, the laser state, and the time take for each section. This file is mainly for record keeping and is not required to stitch the images. It may be used by BakingTray for certain operations, such as resumption of a finished acquisition.

  • The rawData directory is created when acquisition starts. Within it are a series of section directories. Each section directory contains data from one physical section. e.g. if the sample name is AMo_20 you will see:

    $ ls -l rawData
ls -l rawData/
total 0
drwxrwx--- 1 user users 5526 Aug 11 10:29 AMo_20-0001
drwxrwx--- 1 user users 5526 Aug 11 10:31 AMo_20-0002
drwxrwx--- 1 user users 5526 Aug 11 10:32 AMo_20-0003
...

  • Within each section directory you will find the image files. If you are using ScanImage for the acquisition and doing tile-scanning (grid of images) then each TIFF will contain all depths from all channels for each x/y position. So if you have a 3 x 3 tile grid, there will be 9 TIFFs per section directory. Once all tiles have been acquired, an empty file called COMPLETED is added. There is also a file called tilePositions.mat, which contains the position of each tile in the grid (including the stage coordinates reported by the stage). This file is created by the callback function SIBT.tileAcqDone which in a tile scan runs at the conclusion of each X/Y position.

Developer information

  • The recipe file is generated by recipe.writeFullRecipeForAcquisition (the API command is hBT.recipe.writeFullRecipeForAcquisition).

  • The _acqLog_XXX.txt file is created during acquisition by BT.bake.

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