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AbigailMcGovern / iterseg

napari plugin for iteratively improving 3D instance segmentation of cells (u-net x watershed)
BSD 3-Clause "New" or "Revised" License
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Find channel axis #18

Closed jni closed 8 months ago

jni commented 9 months ago

The existing code assumes that the channel axis is the first axis. This is not the case for ome-zarr files. In this PR I instead check for the shortest axis and assume that that contains the channels. This should be safe for most datasets. (And anyway should soon be deprecated in favour of correct metadata on input datasets, see #17.)

jni commented 9 months ago

@AbigailMcGovern even though I think one day we will get rid of load_data, for now I think we should merge this.