BakingTray

What is it?

BakingTray is an open source MATLAB-based serial section 2-photon imaging system inspired by the TeraVoxel (Economo, et al) and MouseLight (Winnubst, et al) projects. The software is for research and development purposes. BakingTray is not scanning software: it is a wrapper around the ScanImage API.

Who is it for?

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 hardware supported by ScanImage.

How does it work?

BakingTray is based upon an existing tile-scanner extension for 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.

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, 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.

Getting started

The software has been tested on MATLAB R2019b to R2021a. It runs on ScanImage 5.6.x and Basic 2020 and 2021. See the documentation at bakingtray.mouse.vision

Please do get in touch if use the software: especially if you are publishing with it!

Related work

• Winnubst et al. Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain. Cell 2019
• Economo et al. A New Platform for Brain-Wide Imaging and Reconstruction of Neurons. eLife 2016
• Li et al. Micro-Optical Sectioning Tomography to Obtain a High-Resolution Atlas of the Mouse Brain. Science. 2010
• Mayerich et al. Knife-edge scanning microscopy for imaging and reconstruction of three-dimensional anatomical structures… J. Microscopy. 2008
• Ragan et al. Serial two-photon tomography for automated ex-vivo mouse brain imaging. Nat. Meth. 2012
• Seiriki, et al. High-Speed and Scalable Whole-Brain Imaging in Rodents and Primates. Neuron 2017
• Zheng et al. Visualization of brain circuits using two-photon fluorescence micro-optical sectioning tomography. Opt. Express. 2013