Stalefish: Spatial ISH Analysis

Stalefish: Spatial ISH Analysis

Seb James (sebjames) Publisher
  • Seb James (sebjames) Publisher
  • Science

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sudo snap install stalefish

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Channel Version Published

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.

Developer website

Details for Stalefish: Spatial ISH Analysis

License
GPL-3.0-or-later
Last updated
12 October 2021

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