Add pyramidal ome-tiff support

jni commented 3 years ago

Christoph Gohlke shared his recipe here:

https://forum.image.sc/t/wholeslide-ome-tiff-in-napari-from-ipython/52872/5

import tifffile
import zarr
import napari

filename = 'HSM0170-20x20.ome.tiff'  # 163 GB compressed

store = tifffile.imread(filename, aszarr=True)
zgroup = zarr.open(store, mode='r')
print(zgroup.info)
print(zgroup[0].info)
data = [
    zgroup[int(dataset['path'])]
    for dataset in zgroup.attrs['multiscales'][0]['datasets']
]

viewer = napari.view_image(data, rgb=True, contrast_limits=[0, 255])
napari.run()
store.close()

GenevieveBuckley commented 3 years ago

PRs welcome!

imagesc-bot commented 7 months ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/napari-ome-tiff-reader/91918/14

GenevieveBuckley commented 3 months ago

Closed by https://github.com/napari/napari-tiff/pull/24

napari / napari-tiff

Add pyramidal ome-tiff support #9