From ee67d25ea1dfb7299536dcb13e8fd17e4a145568 Mon Sep 17 00:00:00 2001 From: William Moore Date: Fri, 23 Jun 2023 13:27:26 +0100 Subject: [PATCH 1/2] Add usage docs to README --- README.md | 43 +++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 41 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 368decf..9b00bfd 100644 --- a/README.md +++ b/README.md @@ -3,5 +3,44 @@ An app for hosting a catalog of OME-Zarr samples: Images and Plates supported. -You provide a list of OME-Zarr URLs and the app loads metadata and displays a -zoomable thumbnail of the image in a table. +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: + +https://ome.github.io/ome-zarr-catalog/?csv=https://raw.githubusercontent.com/ome/ome-zarr-catalog/main/public/zarr_samples.csv + +This adds a single `Thumbnail` column to the data in the `CSV` file. + + + + +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` + + + From 732c4ef70243e4166de24aaf0446e8e8127d5eb0 Mon Sep 17 00:00:00 2001 From: William Moore Date: Fri, 23 Jun 2023 13:29:36 +0100 Subject: [PATCH 2/2] Add link to README --- README.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 9b00bfd..868bd38 100644 --- a/README.md +++ b/README.md @@ -22,10 +22,10 @@ https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr, CC BY 4.0 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: -https://ome.github.io/ome-zarr-catalog/?csv=https://raw.githubusercontent.com/ome/ome-zarr-catalog/main/public/zarr_samples.csv - 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 + @@ -42,5 +42,7 @@ We can specify which columns from the following list to add: 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 +