Alignment of warped atlas to autofluorescence looks correct but overlay of raw atlas with transformed cells appears wrong.

ClearAnatomics / ClearMap

ClearMap 2 with WobblyStitcher, TubeMap and CellMap

https://clearanatomics.github.io/ClearMapDocumentation/

GNU General Public License v3.0

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Alignment of warped atlas to autofluorescence looks correct but overlay of raw atlas with transformed cells appears wrong. #104

Closed andrewsilberfeld closed 2 years ago

andrewsilberfeld commented 2 years ago

My alignments look great (middle, right) but the transform function produces coordinates that don't seem right when I look in my voxelized result (left). Does anyone know why this happened?

andrewsilberfeld commented 2 years ago

this was due to my downsampling/upsampling of cell coordinates prior to transformation which round pixels to nearest 10 (8456 to 8460) which caused improper mapping using transformix. Passing the raw pixels solved the problem.