search

AllenInstitute / biofile-finder

An open-use web application created for easy access, collaboration, and sharing of datasets through rich metadata search, filter, sort, and direct viewing in common industry applications or in our web-based 3D Volume Viewer.
https://biofile-finder.allencell.org/
BSD 3-Clause "New" or "Revised" License
3 stars 1 forks source link

Feature/zarr thumbnails #143

Closed BrianWhitneyAI closed 5 months ago

BrianWhitneyAI commented 5 months ago

Description

The purpose of this PR is to render thumbnails for zarr images. Resolves #89. This includes finding the lowest resolution version and taking a middle slice to ensure the highest possibility of a useful thumbnail.

Issues

This feature is heavily dependent on the access level of the file, often failing with CORS issues. I believe this is all server-side, so if we want to have this feature usable with FMS data we need to adjust those permissions.

Testing

Since we cannot test on existing data in FMS we need to import our data. I used the variance dataset to check this. I was only able to import this dataset successfully on Mac so there still might be some weird things here. If you use the variance dataset then make sure to remove the thumbnail column.

SeanLeRoy commented 5 months ago

Were you able to test out NucMorph files? I sent you one previously via Slack - it would be cool to know it works on other ZARRs beyond those in variance

BrianWhitneyAI commented 5 months ago

Were you able to test out NucMorph files? I sent you one previously via Slack - it would be cool to know it works on other ZARRs beyond those in variance

I tried it with this one https://allencell.s3.amazonaws.com/aics/nuc_morph_data/data_for_analysis/baseline_colonies/20200323_09_small/seg.ome.zarr and the image rendered to download