Acquisition Pipelines
BakingTray: serial-section acquisition software
BakingTray is modular serial-section acquisition software for MATLAB. It can easily be modified to utilize 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 catalyzing developments in serial section imaging than a complete turn-key system.
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.
Custom Projects
Zapit: random-access optogenetics
Zapit is point-based (scanner-based) optostimulator system for head-fixed mouse behavioral tasks. The software will run on a variety of hardware designs and experimental paradigms. A user-friendly MATLAB GUI handles creation of stimulus sets, scanner calibration, and alignment of stereotaxic coordinates to the sample. The experiment itself is run via a MATLAB API: using a small number of simple commands the user can initiate and stop optostimulation, and handle trial logging to disk. There is a Python wrapper for the MATLAB API and support for presenting stimuli in other programming languages. Zapit is a collaboration between the AMF and several SWC labs. Click HERE to read our pre-print.
Software Tools
Visualisation: Lasagna
This Python-based software was originally developed by Rob Campbell for a project with Tom Mrsic-Flogel’s lab, but is now being used by the IBL consortium to trace electrode tracks. It provides linked orthogonal 2-D views for fast visualisation of downsampled image stacks. Allows overlays of multiple brains, multiple channels, traced neurites, or soma locations. Includes viewer for Allen Atlas and is extendable via plugins. Lasagna pre-dates napari, which we would recommend for new projects
Data Acquisition: SimpleMScanner
This MATLAB software was written by Rob Campbell for teaching purposes. It runs galvo-based scanning microscopy using NI Hardware. The project includes three increasingly complicated versions of the same program. An equivalent Python project can be found here. This code can any scanning based microscope, from a simple transmission-based system to a 2-photon.
Visualisation: MaSIV
This MATLAB-based package was developed by Alex Brown in Troy Margrie’s lab. MaSIV is a simple multi-resolution image viewer: it loads a small downsampled image stack into RAM but presents the user with full-res data as they zoom in. MaSIV is stable but can only display a single channel at once. It is extendable via plugins, some of which were written by AMF members.