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NotImplementedError: Multiscale images are not implemented yet #70
Description
Hi, I tried to run the densenet.ipynb notebook, but faced an error when creating ImageTilesDataset: NotImplementedError: Multiscale images are not implemented yet.
The original code is
dataset = ImageTilesDataset( sdata=merged, regions_to_images={"cell_circles": "CytAssist_FFPE_Human_Breast_Cancer_full_image"}, tile_dim_in_units=3 * xenium_circles_diameter, tile_dim_in_pixels=32, target_coordinate_system="aligned", transform=my_transform, )
and was modified to:
dataset = ImageTilesDataset( sdata=merged, regions_to_images={"cell_circles": "CytAssist_FFPE_Human_Breast_Cancer_full_image"}, tile_dim_in_units=3 * xenium_circles_diameter, #tile_dim_in_pixels=32, #target_coordinate_system="aligned", regions_to_coordinate_systems={"cell_circles": "aligned"}, transform=my_transform, )
with spatialdata version=0.0.16.dev24+ga5336d8 installed from GitHub.
Do you have any suggestions for this issue? Thank you.
Activity
LucaMarconato commentedon Jan 16, 2024
Thanks for reporting, we tested the notebook before making a release so it should work on the latest version of spatialdata and we are aware that it currently doesn't work on the main branch. In fact we improved the
ImageTilesDatasetclass with this PR scverse/spatialdata#299 but we haven't updated the notebook yet.I will do this before the next release, but also I will keep you updated here as soon as it is ready, so that you don't have to wait for the next release.
LucaMarconato commentedon Mar 20, 2024
@duongvtt96, with scverse/spatialdata#439 merged, the new
ImageTilesDatasetclass now work also for multiscale images and multiscale labels. I will update the example notebook for the 0.1.0 release but you can already use the code if you installspatialdatafrom themainbranch.