Merge branch 'dev' of https://github.com/NFDI4BIOIMAGE/omero-vitessce …

…into dev
NFDI4BIOIMAGE · Nov 8, 2024 · 61928bd · 61928bd
2 parents 0a08615 + adaedec
commit 61928bd
Showing 1 changed file with 15 additions and 8 deletions.
diff --git a/README.md b/README.md
@@ -5,7 +5,7 @@
 OMERO.omero_vitessce
 =======================
 
-OMERO Vitessce multimodal data viewer.
+OMERO-vitessce is an OMERO.web plugin for the [Vitessce](http://vitessce.io/) multimodal data viewer. 
 
 Installation
 ============
@@ -39,7 +39,7 @@ Now restart OMERO.web as normal for the configuration above to take effect.
 
 ### omero-web-zarr
 While [omero-web-zarr](https://github.com/ome/omero-web-zarr) is not a requirement, but it is strongly recommended to have it installed and enabled for using this plugin
-omero-web-zarr is necessary to take advantage fully of the autogenerated config files for the Vitessce viewer,
+omero-web-zarr is necessary to take advantage of the autogenerated config files for the Vitessce viewer,
 as they rely on omero-web-zarr to serve the images to the viewer.
 
 Please see https://pypi.org/project/omero-web-zarr/ for instructions on installing and enabling the omero-web-zarr plugin.
@@ -88,7 +88,7 @@ Config files can be generated for:
 - `datasets`
 
 Assumes that [omero-web-zarr](https://github.com/ome/omero-web-zarr) is available to serve the images.
-The attachements must be in `.csv` format and the column with the cell identifiers should be consistent across attachements.
+The attachements must be either [OMERO.tables](https://omero.readthedocs.io/en/stable/developers/Tables.html) or files in`.csv` format and the column with the cell identifiers should be consistent across attachements.
 Only files attached to the dataset/image are available in the form.
 
 The following fields are available:
@@ -97,14 +97,14 @@ The following fields are available:
 - `Images`               (required): 	                                       OMERO Image(s) to view, assumes the same pixel size for all images.
 - `Segmentation`        (optional, `None`): 	                               Label image to overlay on the image, pixel values correspond to cell identities.
 - `ROIs`                (optional, `False`):                                   Use the ROIs from OMERO as a cell segmentation. Assumes 1 polygon/rectangle shape per ROI, whose text value is the cell identity.
-- `Cell identities`     (optional, `None`): 	                               `.csv` file with at least 2 columns: `Cell id column` and `Label column` defined in the 2 fields below. 
+- `Cell identities`     (optional, `None`): 	                               `.csv` file / OMERO.table with at least 2 columns: `Cell id column` and `Label column` defined in the 2 fields below. 
 - `Cell id column`      (optional, "cell_id"):   	                           Name of the `Cell id column` used in `Cell identities`, `Expression`, `Embeddings`.
 - `Label column`        (optional, "label"): 	                               Name of the `Label` used in `Cell identities`.
-- `Expression` 	      (optional, `None`):                                  `.csv` file with the `Cell id column` all other columns are considered as expression values and should be numerical.
-- `Embeddings`          (optional, `None`):                                  `.csv` file with the `Cell id column` and the `Embedding x` and `Embedding y` columns defined in the 2 fields below. 
+- `Expression` 	      (optional, `None`):                                  `.csv` file / OMERO.table with the `Cell id column` all other columns are considered as expression values and should be numerical.
+- `Embeddings`          (optional, `None`):                                  `.csv` file / OMERO.table with the `Cell id column` and the `Embedding x` and `Embedding y` columns defined in the 2 fields below. 
 - `Embedding x`         (optional, "UMAP_1"): 	                            Name of the `Embedding x` used in `Embeddings`.
 - `Embedding y`         (optional, "UMAP_2"): 	                            Name of the `Embedding y` used in `Embeddings`.
-- `Molecules`           (optional, `None`): 	                               `.csv` file with at least 4 columns: Molecule id, label, x, y (headers in the fields below). 
+- `Molecules`           (optional, `None`): 	                               `.csv` file / OMERO.table with at least 4 columns: Molecule id, label, x, y (headers in the fields below). 
 - `Molecule id`         (optional, "id"):   	                                Name of the `Molecule id column` used in `Molecules`.
 - `Molecule label`      (optional, "gene"):   	                            Name of the `Molecule label column` used in `Molecules`.
 - `Molecule x`          (optional, "x"):   	                                Name of the `Molecule x column` used in `Molecules`.
@@ -124,6 +124,12 @@ The `Status` panel will be empty unless a `Segmentation` or `Embeddings` are pro
 The `ROIs` are used as cells. Only the first shape is considered, and only polygons and rectangles are kept (TO DO: add support for ellipses). Other shapes are skipped.
 The text value of the shape is used as a cell identity to link with expression/labels/embeddings, if there is no text value the ROI is skipped.
 
+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): 
+
 #### Attaching preexisting config files
 Custom config files should have a `.json` extension and added as attachements to a dataset or an image.
 The configuration files does not need to refer to the dataset / image it is attached to and can refer to other images.
@@ -137,7 +143,8 @@ 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).
-- `omero_vitessce/vitessce_json_rois/ID1,ID2,...` endpoint where `ID1,ID2,...` is a comma-separated list of image ids.
+- `webclient/omero_table/ID/csv/` endpoint (ID = OMERO file ID of the OMERO.table): 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:
 ![image](https://github.com/user-attachments/assets/223072d6-9aa7-4b96-a199-65bbab863c1b)