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ome-zarr-catalog

An app for hosting a catalog of OME-Zarr samples: Images and Plates supported.

You provide a list of OME-Zarr samples as a CSV table and the app loads metadata and displays a thumbnail of each image in a table.

The apps is deployed at https://ome.github.io/ome-zarr-catalog/. You simply need to specify the location of your CSV file after the URL as `?csv=URL_to_your_table.csv.

For example a CSV file like this is hosted in this repo under public/zarr_samples.csv.

URL,                                                                   License,    Study,    Date added
https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0054A/5025553.zarr,   CC BY 4.0,  idr0054,  2022-06-03
https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0076A/10501752.zarr,  CC BY 4.0,  idr0076,  2022-06-21
https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0047A/4496763.zarr,   CC BY 4.0,  idr0047,  2022-06-21
https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr,   CC BY 4.0,  idr0062,  2022-06-21

It's raw URL is https://raw.githubusercontent.com/ome/ome-zarr-catalog/main/public/zarr_samples.csv and we can use that to display it as a catalog page:

This adds a single Thumbnail column to the data in the CSV file.

See https://ome.github.io/ome-zarr-catalog/?csv=https://raw.githubusercontent.com/ome/ome-zarr-catalog/main/public/zarr_samples.csv

We can specify which columns from the following list to add:

  • Version - Adds a column with the OME-NGFF version
  • Axes - Displays the axes of the Image
  • shape - Displays the shape of the Zarr data at highest resolution
  • chunks - Displays the chunks of the Zarr data at highest resolution
  • Wells - Shows the Well count for Plate data
  • Fields- Shows the Fields count for Plate data
  • Keywords - Adds labels paths, plate and/or bioformats2raw.layout
  • Thumbnail - Renders the smallest multiscales dataset as a Thumbnail

These can be specified as a URL query string, e.g. ...&columns=Axes,Thumbnail,shape,chunks

See https://ome.github.io/ome-zarr-catalog/?csv=https://raw.githubusercontent.com/ome/ome-zarr-catalog/main/public/zarr_samples.csv&columns=Axes,Thumbnail,shape,chunks