search

hms-dbmi / viv

Library for multiscale visualization of high-resolution multiplexed bioimaging data on the web. Directly renders Zarr and OME-TIFF.
http://avivator.gehlenborglab.org
MIT License
288 stars 46 forks source link

Multi-series ome-tiff #831

Open gouinK opened 1 month ago

gouinK commented 1 month ago

User story I have both RGB and standard grayscale images that I would like to be able to switch between in Viv. From my testing, it seems that Viv cannot parse multi-series ome-tiffs, though it certainly is possible that I overlooked something.

Preferred solution I have created an ome-tiff that contains two series, one for all of the RGB images and another for all of the grayscale images. The first series' photometric attribute is set to RGB and the second series' photometric attribute is set to MINISBLACK. It would be great if Viv could support this type of input.

Possible alternatives None so far.

ilan-gold commented 1 month ago

@gouinK Could you be a bit more specific? Perhaps a link to the OME data model you're referring to? I am not as fast anymore with this stuff so could use the refresher. For example https://avivator.gehlenborglab.org/?image_url=https://viv-demo.storage.googleapis.com/2018-12-18_ASY_H2B_bud_05_3D_8_angles.ome.tif renders correctly and it has multiple independent images?