PhysicalSize and 3D ome-zarr-py


I was looking at the image from the ome-zarr-py tutorial in 3D and in Avivator. I noticed that the ratio of PhysicalSizeZ to PhysicalSizeX and PhysicalSizeY is large (reported here: Webclient). It is about 1.5 times larger in Z than in the other dimensions but the 3D visualization in napari does not quite look like this. Should the image volume in theory be scaled? Just wondering… Also, I could not view the volume from the remote data - I had to download it. Otherwise Napari crashed with UserWarning: resource_tracker: There appear to be 3 leaked semaphore objects to clean up at shutdown
  warnings.warn('resource_tracker: There appear to be %d '

cc @joshmoore @will-moore

I have disabled the setting of Z scale metadata in ome-zarr-py because at the time, this resulted in the number of steps on the Z-slider in napari to be different from the number of Z slices, E.g. 50 Z-sections but only 30 Z-slider increments. So that you couldn’t select every Z slice using the slider. See discussion at Napari non-integer step size - #4 by jni

This may have been improved in napari since then, so I’ll have another look.


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Yup, I think you’re good to set it now, @will-moore! Also, I didn’t know the ome-zarr-py format let one specify scale???

I got the scaling from an OME-TIFF file that I generated from the originally uploaded data via bfconvert which has the metadata. Would be cool if ome-zarr(-py) supported it!

Sorry, yes you’re right. ome-zarr-py doesn’t yet support scale since it’s not yet in the OME-Zarr spec. I was thinking of omero-napari where we have scale info from OMERO. But Voxel size is very high on our TODO list for #ngff.