BakingTray Documentation
Serial-section 2-photon microscopy for everyone
BakingTray is a complete open source software platform for serial section 2-photon tomography. This technique allows 3D volumetric imaging of uncleared samples at high resolution and with minimal user input. BakingTray was developed at the Sainsbury Wellcome Centre Advanced Microscopy Facility, where it runs our BrainSaw microscopes and has helped us image over 7,000 brains in the last decade.
Who is it for?
This software is aimed at technically-minded people who want to set up serial section 2-photon tomography in their lab or imaging facility. A dozen BrainSaws have been built world-wide to date. BakingTray will run on any microscope hardware supported by ScanImage. An existing two-photon microscope can be upgraded to run BakingTray from about 35,000 EUR (depending on existing hardware). A legacy TissueCyte 1000 can be upgraded to BakingTray for around 35,000 to 65,000 EUR depending on what additional features you choose to add.
Features
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 for images.
How to get it?
Find the project on GitHub and start with the build overview.
How to cite it?
If you use BakingTray in your research, please cite our methods paper. See Citing BakingTray for a suggested acknowledgement, an example methods section, and the full reference list.
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