https://github.com/comparative-pathology/gcamodelscripts

Various small image processing scripts used with Gut Cell Atlas models.

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Various small image processing scripts used with Gut Cell Atlas models.

Created about 5 years ago · Last pushed almost 2 years ago

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Various small image processing scripts used with Gut Cell Atlas models. Most of which are probably written using Python and probably use PyWoolz.

GCAConvertHubmapPlacement.py - Converts JSON encoded sample placements downloaded from HuBMAP to JSON encoded Edinburgh Gut Cell Atlas landmark bounded proportional distance intervals.
GCAExtractColonPath.py - extracts the colon path from a Woolz segmented colon domain.
GCAXY2SplineIndex.py - creates a single Woolz object in which the values are the spline index values corresponding to the x, y coordinate values in coordinate value objects.
GCAMapHuBMAPSampleDomains.py - computes the 3D spatial mapping of a HuBMAP Large Intestine sample to a HuBMAP (v1.1) large intestine model.

These scripts were developed for use by the Gut Cell Atlas Project funded by the Helmsley Charitable Trust.