[BHEU2024] Fix bioimage_inference tool with 3D images #1544
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@anuprulez Any idea what might be going on here? |
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@kostrykin I had a look into 3DUNetArabidopsisApicalStemCells.pt and its RDF file. In the RDF file, the
but when I load the NPY file, it is actually 5-dimensional. The 5-dimensional file works as correct test data with the associated Pytorch model. In the Galaxy tool, I use the information from the RDF file to find the right number and order of dimensions. But, for this 3DUNetArabidopsisApicalStemCells 3D mode, it seems to be different to me. Do we have separate information that can be used to provide the model to find the correct number of input file dimensions?
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The tool yields an error when we try to use a 3D image. For example, using the 3DUNetArabidopsisApicalStemCells.pt model and an image with shape
256,256,2,1yields the error:Original PR for this tool: #1391
xref beatrizserrano/galaxy-image-community#26