BakingTray Documentation

Serial-section extension for ScanImage

BakingTray is an open source ScanImage wrapper written at the Sainsbury Wellcome Centre Microscopy Facility for performing automated serial-section tile scanning within MATLAB. BakingTray was inspired by the TeraVoxel (Economo, et al) and MouseLight (Winnubst, et al) projects and is made public for research and development purposes.

Who is it for?

BakingTray is not scanning software: it is a wrapper around the ScanImage API. This software is aimed at technically-minded people who want to experiment with serial-section imaging and have full control over all aspects of the process. Setting up BakingTray from scratch on your rig requires significant effort, good MATLAB programming skills, knowledge of ScanImage, and the know-how to set up and run a 2-photon microscope. This is not a turn-key solution. BakingTray will run on any microscope hardware supported by ScanImage.

How does it work?

BakingTray is based upon an existing tile-scanner extension for ScanImage, simply adding the ability to slice the sample after each section. Imaging itself is performed via ScanImage, which is freely available MATLAB-based software for running 2-photon microscopes.

Current features

This software has been thoroughly stress-tested and is capable of generating production-quality data. The current feature set is as follows:

  • Easy sample set up: take a fast preview image of the sample then draw a box around the area to be imaged. An Auto-ROI feature is available for adaptively imaging only the tissue.

  • Acquisition of up to four channels using resonant or linear scanning.

  • A low-resolution preview image of the current section is assembled in real time.

  • Graceful acquisition abort (either immediately or at the end of the current section) and pausing.

  • Automatically halts if the laser drops out of modelock.

  • PMTs and laser automatically switch off at the end of the acquisition.

  • Support for multiple lasers via Scanimage.

  • Easy control of illumination as a function of depth via ScanImage.

  • Integrates with our StitchIt software for assembling the stitched images from raw tiles.

  • Easily resume a previously halted acquisition.

  • Imaging of multiple samples at once.

  • Modular API allows developers to easily extend the software or adapt it to different hardware.

  • Slack messages on acquisition completion.

What do the results look like?

See the Gallery.

How to get it?

Find the project on GitHub.

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