Stalefish: Spatial ISH Analysis banner


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. For more details see (paper coming soon).

Significant contributions to this software were made by Mackenzie Englund (original concept and Python implementation of polynomial curve fitting) and Stuart Wilson (initial 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 was developed by Seb James.


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