From adaedeceba32ea1cd38b3d25824b7add271bd818 Mon Sep 17 00:00:00 2001 From: Michele Bortolomeazzi Date: Thu, 7 Nov 2024 16:42:44 +0100 Subject: [PATCH] Update README.md --- README.md | 23 +++++++++++++++-------- 1 file changed, 15 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index a1aeef7..ec2a063 100644 --- 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)