BrainSaw Serial Section 2-photon
Open platform for serial-section 2-photon tomography
What is serial-section two-photon microscopy?
Block-face serial two-photon tomography (STPT) provides high-resolution, whole-organ volumetric imaging whilst avoiding complex sample preparation. In an STPT system, a multi-photon microscope is coupled to a vibratome and a three-axis stage. Fixed tissue is embedded in agarose and mounted in a water bath riding on the stage. The tissue surface is exposed by the vibratome and tile-scanned by the 2-photon microscope. The STPT system alternates between slicing and imaging of the block face until all of the sample has been acquired.
STPT is ideal for reliable high-throughput whole-brain imaging; we have acquired about 8,000 brains since 2018 using our in-house "BrainSaw" serial-section platform. The AMF has three open-source BrainSaw microscopes and about a dozen more have been built by others worldwide (see interactive map on the right). BrainSaw has contributed to over 30 research papers and is routinely used for tasks such as mapping electrode tracks or whole-brain cell counting. Up to 6 brains can be imaged overnight on a single microscope; the process is fully automated and highly reliable.
Ecosystem
BrainSaw: microscopy systems
We provide CAD models and build instructions for assembling a BrainSaw serial-section two-photon microscope. Systems can be built from scratch, or serial-sectioning functionality added to an existing microscope. We have three BrainSaw systems in-house: NeuroVision, BrainSaw OG, and OrganGrinder.
BakingTray: serial-section acquisition software
BakingTray is modular serial-section acquisition software for MATLAB. It accommodates diverse hardware configurations and acquires images via ScanImage.
Docs
StitchIt: assembling tile scan data into stitched sections
StitchIt runs alongside BakingTray to pre-process data during acquisition, stream the last stitched section to a web page, and initiate stitching automatically when acquisition completes. It includes tools for downsampling and batch-processing image stacks, with operations highly parallelised for speed.
Docs
BrainSaw Channel Chooser
This interactive web tool helps BrainSaw users choose the best wavelength and excitation channels for their fluorophores.
Launch
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.
WWWVideo: BakingTray in action
This video shows acquisition of a single section on a BrainSaw serial-section two-photon microscope using BakingTray acquisition software. The video was acquired at the Sainsbury Wellcome Centre Advanced Microscopy Facility. We see acquisition of four mouse brains near the start of the process, at the cerebellum. More details available on the YouTube page.