BrainSaw Serial Section 2-photon
Open tools for acquiring and stitching serial section data
"BrainSaw" is the generic term for our in-house serial section 2-photon systems. BrainSaw systems run "BakingTray" acquisition software backed up by the "StitchIt" pre-processing and stitching pipeline. BrainGlobe tools can be used to analyse the results. This platform has contributed to over 30 research papers and some 10 BrainSaw clones exist outside of the SWC.
BakingTray: serial-section acquisition software
BakingTray is modular serial-section acquisition software for MATLAB. It can easily be modified to utilise any desired acquisition hardware (scanners, stages, etc). Images are currently acquired with ScanImage, but BakingTray can easily be extended to work with any acquisition system (e.g. a spinning-disk confocal or your own scanning software). BakingTray is more of a research platform for catalysing developments in serial section imaging than a complete turn-key system.
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StitchIt: assembling tile scan data to stitched sections
Pre-processes data during acquisition, streams the last stitched section to a web page, initiates stitching automatically when acquisition completes. Includes tools for downsampling and generally batch-processing image stacks. Operations highly parallelized for speed.
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Analysis: BrainGlobe
Our favoured option for analysis of serial section data is the BrainGlobe suite. These Python-based tools are maintained by the SWC neuroinformatics team. BrainGlobe comprises several software packages to access, analyse and visualise anatomical data. The packages are interoperable in order to streamline the process of going from raw data to publication-ready content.
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