BakingTray is a complete software platform for 2-photon serial tomography STPT. It plugs into ScanImage and runs within MATLAB. For more information see the SWC AMF BrainSaw project page.
This software is aimed at technically-minded people who want to build their own STPT system 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. BakingTray will run on any hardware supported by ScanImage.
BakingTray simply slices off the top of the sample after each tile-scan is complete, exposing fresh tissue for imaging. Imaging itself is performed via ScanImage, which is freely available MATLAB-based software for running 2-photon microscopes.
This software has been thoroughly stress-tested and is being run in several labs and facilities worldwide. The current feature set is as follows:
- Easy sample set up: take a fast preview image of the sample, draw a box around the area to be imaged, "auto-ROI" feature for imaging only the sample.
- 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 switched 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.
- Modular API allows developers to easily extend the software or adapt it to different hardware.
- Slack messages on acquisition completion.
The software has been tested on MATLAB R2019b to R2021a. It runs on ScanImage 5.6.x but the latest version of Basic is preferred. See the documentation at bakingtray.swcmicroscopy.com
Please do get in touch if use the software: especially if you are publishing with it!