The AMF actively develops software tools related to microscope acquisition and behavior. All tools are developed in the open and we are always happy to collaborate. Click our GitHub link, above, to see some of what we do. In addition to tools developed within the AMF, we collaborate with others to develop shared tools. Examples of collaborative work includes:
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.