Neuroscience tool to make 3D reconstructions from brain slice images
Stalefish is a tool to analyse gene expression. From your brain slice images you can build 3D
expression surfaces and then convert these into 2D expression maps or save them in GL transmission format (glTF). For more details see the preprint: https://www.biorxiv.org/content/10.1101/2021.07.28.454203v1.
Significant contributions to this software were made by Mackenzie Englund (original concept and Python implementation of polynomial curve fitting) and Stuart Wilson (initial C++ implementation of polynomial fitting and box-based luminance sampling using OpenCV). Bezier curve fitting, slice alignment algorithms, 3D visualization, 3D to 2D digital unwrapping and alignment of maps to a common coordinate alignment were developed by Seb James.
For versions of Ubuntu between 14.04 LTS (Trusty Tahr) and 15.10 (Wily Werewolf), as well as Ubuntu flavours that don’t include snap by default, snap can be installed from the Ubuntu Software Centre by searching for snapd.
Alternatively, snapd can be installed from the command line:
sudo apt update
sudo apt install snapd
Either log out and back in again, or restart your system, to ensure snap’s paths are updated correctly.
Install Stalefish: Spatial ISH Analysis
To install Stalefish: Spatial ISH Analysis, simply use the following command: