From 690fc1181698aaa942f002e42437b05f7041eb2b Mon Sep 17 00:00:00 2001 From: Michele Bortolomeazzi Date: Fri, 8 Nov 2024 18:16:32 +0100 Subject: [PATCH] Update README.md --- README.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index ec2a063..3cd5374 100644 --- a/README.md +++ b/README.md @@ -128,7 +128,9 @@ OMERO.tables for use with omero-vitessce can be generated with: - OMERO python API (https://omero.readthedocs.io/en/stable/developers/Tables.html) or ezomero (https://thejacksonlaboratory.github.io/ezomero/ezomero.html#ezomero.post_table) - Fiji (https://wiki-biop.epfl.ch/en/data-management/omero/omero-tables#create-omerotables-from-a-fiji-script) - QuPath (https://wiki-biop.epfl.ch/en/data-management/omero/qupath#annotations-measurement-tables) -- other [tools](https://omero-guides.readthedocs.io/en/latest/external_tools.html) / [APIs](https://omero-guides.readthedocs.io/en/latest/api_usage.html): +- other [tools](https://omero-guides.readthedocs.io/en/latest/external_tools.html) / [APIs](https://omero-guides.readthedocs.io/en/latest/api_usage.html): + +OMERO.tables with a number of rows > `omero.web.max_table_download_rows` (default `10000`) will be truncated, and the value ignored by omero-vitessce. #### Attaching preexisting config files Custom config files should have a `.json` extension and added as attachements to a dataset or an image. @@ -143,7 +145,7 @@ Images and data can be served through: - [omero-web-zarr](https://pypi.org/project/omero-web-zarr/): OME-NGFF images only. - [omero-openlink](https://github.com/sukunis/OMERO.openlink): all images and file attachements. - `webclient/annotation/` endpoint: only for Annotations (useful for file attachments). -- `webclient/omero_table/ID/csv/` endpoint (ID = OMERO file ID of the OMERO.table): for getting OMERO.tables as `csv` files. +- `webclient/omero_table/ID/csv?limit=MAX_TABLE_DOWNLOAD_ROWS` endpoint (`ID` = OMERO file ID of the OMERO.table, `MAX_TABLE_DOWNLOAD_ROWS` = the OMERO.web setting): for getting OMERO.tables as `csv` files. - `omero_vitessce/vitessce_json_rois/ID1,ID2,...` endpoint where `ID1,ID2,...` is a comma-separated list of image ids, to get the first shape of each ROI in `json` format. Example showing ROIs from OMERO displayed in the omero-vitessce viewer window: