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ClearAnatomics / ClearMap

ClearMap 2 with WobblyStitcher, TubeMap and CellMap
https://clearanatomics.github.io/ClearMapDocumentation/
GNU General Public License v3.0
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Start process at step binary_filled: IndexError: index _ is out of bounds for axis 0 with size _ #76

Open marion-giraud opened 3 years ago

marion-giraud commented 3 years ago

Hello,

I use ClearMap on personal lighsheet microscopy vascular dataset. Before doing the skeletonization, I would like to add a post-treatment after the filling. For now, I extract the binary_filled.npy as tiff files, treat them and save as a new binary_filled.tif that I convert to npy file. But when I want to apply the skeletonization and graph creation this new binary_filed.npy I have the following error:

issue_index

If I start the process from binary_filled.npy without a post treatment, I do not have the error.
I suppose that it is linked to the way the binary filled array is stored, but I do not understand what do I have to change.

Thank you very much if you can help me on this matter.

Marion Giraud

crousseau commented 1 year ago

@marion-giraud How do you do the file conversion ? Do you use ClearMap.IO.IO ?