From 768e00ae4ca98cef7a7e8e0eb75390104da089da Mon Sep 17 00:00:00 2001 From: William Moore Date: Mon, 28 Oct 2024 14:22:18 +0000 Subject: [PATCH 1/2] Update README page with link to samples viewer and update validator links --- README.md | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index ea29adb..b108560 100644 --- a/README.md +++ b/README.md @@ -25,7 +25,11 @@ Project planning and material repository for the 2024 challenge to generate 1 PB -of OME-Zarr data +of OME-Zarr data. + +UPDATE (20th October 2024): The data converted for the challenge can now be +browsed and searched at +[https://ome.github.io/ome2024-ngff-challenge/](https://ome.github.io/ome2024-ngff-challenge/). ## Challenge overview @@ -58,30 +62,26 @@ $ mc ls -r uk1anon/idr/share/ome2024-ngff-challenge/0.0.5/6001240.zarr/ [2024-08-01 14:24:28 CEST] 2.7KiB STANDARD zarr.json ``` -The dataset (from idr0062) can be inspected using a development version of the -OME-NGFF Validator available at - - Other samples: -- [4496763.zarr](https://deploy-preview-36--ome-ngff-validator.netlify.app/?source=https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/4496763.zarr) +- [4496763.zarr](https://ome.github.io/ome-ngff-validator/?source=https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/4496763.zarr) Shape `4,25,2048,2048`, Size `589.81 MB`, from idr0047. -- [9822152.zarr](https://deploy-preview-36--ome-ngff-validator.netlify.app/?source=https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/idr0083/9822152.zarr) +- [9822152.zarr](https://ome.github.io/ome-ngff-validator/?source=https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/idr0083/9822152.zarr) Shape `1,1,1,93184,144384`, Size `21.57 GB`, from idr0083. -- [9846151.zarr](https://deploy-preview-36--ome-ngff-validator.netlify.app/?source=https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/idr0048/9846151.zarr) +- [9846151.zarr](https://ome.github.io/ome-ngff-validator/?source=https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/idr0048/9846151.zarr) Shape `1,3,1402,5192,2947`, Size `66.04 GB`, from idr0048. -- [Week9_090907.zarr](https://deploy-preview-36--ome-ngff-validator.netlify.app/?source=https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/idr0035/Week9_090907.zarr) +- [Week9_090907.zarr](https://ome.github.io/ome-ngff-validator/?source=https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/idr0035/Week9_090907.zarr) plate from idr0035. -- [l4_sample/color](https://deploy-preview-36--ome-ngff-validator.netlify.app/?source=https://data-humerus.webknossos.org/data/zarr3_experimental/scalable_minds/l4_sample/color) +- [l4_sample/color](https://ome.github.io/ome-ngff-validator/?source=https://data-humerus.webknossos.org/data/zarr3_experimental/scalable_minds/l4_sample/color) from WebKnossos. - Plates from idr0090: - [190129.zarr](https://deploy-preview-36--ome-ngff-validator.netlify.app/?source=https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/idr0090/190129.zarr) + [190129.zarr](https://ome.github.io/ome-ngff-validator/?source=https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/idr0090/190129.zarr) Size `1.0 TB`, - [190206.zarr](https://deploy-preview-36--ome-ngff-validator.netlify.app/?source=https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/idr0090/190206.zarr) + [190206.zarr](https://ome.github.io/ome-ngff-validator/?source=https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/idr0090/190206.zarr) Size `485 GB`, - [190211.zarr](https://deploy-preview-36--ome-ngff-validator.netlify.app/?source=https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/idr0090/190211.zarr) + [190211.zarr](https://ome.github.io/ome-ngff-validator/?source=https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/idr0090/190211.zarr) Size `704 GB`. -- [76-45.zarr](https://deploy-preview-36--ome-ngff-validator.netlify.app/?source=https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/idr0010/76-45.zarr) +- [76-45.zarr](https://ome.github.io/ome-ngff-validator/?source=https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/idr0010/76-45.zarr) plate from idr0010
Expand for more details on creation of these samples From b22f52853f3facb3b79afc80598d16262da8c65a Mon Sep 17 00:00:00 2001 From: William Moore Date: Mon, 28 Oct 2024 14:46:24 +0000 Subject: [PATCH 2/2] format bold --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index b108560..a8f3de4 100644 --- a/README.md +++ b/README.md @@ -27,7 +27,7 @@ Project planning and material repository for the 2024 challenge to generate 1 PB of OME-Zarr data. -UPDATE (20th October 2024): The data converted for the challenge can now be +**UPDATE (20th October 2024)**: The data converted for the challenge can now be browsed and searched at [https://ome.github.io/ome2024-ngff-challenge/](https://ome.github.io/ome2024-ngff-challenge/).