OMERO.omero_vitessce
=======================
OMERO-vitessce is an OMERO.web plugin for the [Vitessce](http://vitessce.io/) multimodal data viewer.
Installation
============
This section assumes that an OMERO.web is already installed.
Install the app using [pip](https://pip.pypa.io/en/stable/):
NB: You need to ensure that you are running `pip` from the python environment
where `omero-web` is installed.
$ pip install -U omero-vitessce
Add the app to the `omero.web.apps` setting:
$ omero config append omero.web.apps '"omero_vitessce"'
Add `omero_vitessce` as a tab in the right-hand-side panel:
$ omero config append omero.web.ui.right_plugins '["Vitessce", "omero_vitessce/webclient_plugins/right_plugin.vitessce.js.html", "vitessce_tab"]'
Add `omero_vitessce` as an open-with option:
omero config append omero.web.open_with '["omero_vitessce", "open_vitessce", {"supported_objects": ["project", "dataset", "image"], "label": "Vitessce"}]'
Add the omero web address (replace ´'"http://localhost:4080"'´ with your address):
$ omero config set omero.web.omero_vitessce.serveraddress '"http://localhost:4080"'
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 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.
Usage
============
### Selecting the viewer
The plugin can be used with:
- `Vitessce` Tab on the right hand side panel.
- `Open with` `->` `Vitessce` on the left side panel.
#### Right-hand-side panel:
- **Prexisting config files**:
Clicking the link will open a new tab with the viewer displaying the selected configuration.
- **Generating custom config files**:
The form allows the user to automatically generate a config file with the selected parameters. After clicking the `Generate Config` button
a config file is generated and attached to the dataset/image. The viewer displaying the autogenerated configuration will open in a new tab.
#### Open-with:
Right click on a `dataset` or an `images` in the left-panel and select `open-with` -> `Vitessce`.
This will open the vitessce viewer in a new tab using the first configuration file attachement.
### Viewer window
After autogenerating or selecting a config file, the Vitessce viewer is opened in a new tab:
The viewer panels can also be rearranged to better fit the image type/size.
### Config files
The omero-vitessce plugin considers all files with the `.json` extension attached to the image or dataset as config files for the viewer.
The config files should follow the vitessce view-config-json format: http://vitessce.io/docs/view-config-json/
#### Custom config files generated from the right-tab
Config files can be generated for:
- `images`
- `datasets`
Assumes that [omero-web-zarr](https://github.com/ome/omero-web-zarr) is available to serve the images.
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:
- `Save Config` (required, `True`): Save the viewer configuration as an attahment to the current Image/Dataset before launching the viewer.
- `Config file name` (optional, "VitessceConfig-YYYY.MM.DD_HHMMSS.json"): Name of the config file to attach, a ".json" extension is added if missing.
- `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 / 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 / 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 / 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`.
- `Molecule y` (optional, "y"): Name of the `Molecule y column` used in `Molecules`.
- `Histograms` (required , `True`): Add 3 plots showing: The number of transcripts per cell, the number of cells in each set, gene expression in each set.
- `Heatmap` (required , `True`): Adds an heatmap.
- `Status` (required , `False`): Adds a status panel to display info on the selected cell.
- `Description` (required , `False`): Adds a description panel to display info on the dataset/image (taken from the description metadata field from OMERO).
The `Config file name` field depends on the `Save Config` field. When the `Save Config` field is not checked, the `Config file name` field is disabled and its value ignored.
The `ROIs` and `Segmentation` fields are mutually exclusive, when the ROI field is selected the segmentation image is not considered.
The `Expression` and `Cell identities` files are required to show the histograms.
The `Embeddings` file is necessary to show the cells in a scatterplot.
The `Molecules` file is used to overlay molecules on the image. All molecules are displayed and selecting by gene is not yet possible.
The `Status` panel will be empty unless a `Segmentation` or `Embeddings` are provided.
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):
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.
The configuration files does not need to refer to the dataset / image it is attached to and can refer to other images.
For how to create a custom config file see:
- [VItessce Docs](http://vitessce.io/docs/view-config-json/)
- [Vitessce Examples](http://vitessce.io/examples/)
#### Serving the images / rois / data / metadata
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?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:
Development
=======================
## Sources
The main sources this project relies on are:
- omero-vitessce from Will Moore for handling ROIs: https://github.com/will-moore/omero-vitessce
- cookiecutter-omero-webapp: https://github.com/ome/cookiecutter-omero-webapp
- `react_webapp` from omero-web-apps-examples: https://github.com/ome/omero-web-apps-examples/tree/master/react-webapp
- Vitessce python package used for generating config files http://python-docs.vitessce.io/
- omero-web-zarr to serve OME-NGFF images: https://github.com/ome/omero-web-zarr
- omero-openlink to serve images and other files: https://github.com/sukunis/OMERO.openlink
- omero-test-infra for testing: https://github.com/ome/omero-test-infra
## Tests
### Test dataset
The dataset used for automated testing is at: [test/data/MB266](test/data/MB266)
This is a cropped version derived from larger images and their associated data available at:
https://doi.org/10.5281/zenodo.13832665
The original data are available at:
https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1093
The associated publication is available at:
https://www.biorxiv.org/content/10.1101/2024.04.03.586404v1
### omero-test-infra configuration
[omero-test-infra](https://github.com/ome/omero-test-infra) is used for automated tests with [github-actions](.github/workflows/omero_plugin.yml).
The workflow setups an omero installation in docker and then:
1) Runs [app-config](.omeroci/app-config) to set up the omero-web plugin configuration.
2) Runs [app-build](.omeroci/app-build) which:
- runs to create a test user/group and upload a [test dataset](test/data/MB266).
- runs pytest tests in: [test/integration](test/integration)
It is possible to perform these tests locally by:
1) Starting the docker daemon.
2) Cloning the omero-test infra repository inside the base folder of omero-vitessce: `git clone https://github.com/openmicroscopy/omero-test-infra .omero`
3) Running: `.omero/app-docker`
## React web app
### omero_vitessce web app
We serve a custom version of the vitesce app: http://vitessce.io/
The app sets up a vitessce view configured through a text file in json format: http://vitessce.io/docs/view-config-json/
The configuration file is taken from the `?config` url parameter.
### Installation
This project was created with [Create React App](https://github.com/facebook/create-react-app).
You can run this project in development mode or as an OMERO.web Django app.
To get started:
$ cd vitessce_app
$ npm install
In the project directory, you can run:
### `npm start`
Runs the app in the development mode.<br>
Open [http://localhost:3000](http://localhost:3000) to view it in the browser.
The page will reload if you make edits.<br>
You will also see any lint errors in the console.
### `npm run build`
Builds the app for production to the `build` folder and copies the
html and static files to the Django app in `vitessce app`. See the [deploy_build.sh]() script.<br>
You also need to install the app into your `omero-web` environment:
# cd to the root of the repo
$ pip install -e .
You will need to have the app configured in your OMERO.web install:
$ omero config append omero.web.apps '"omero_vitessce"'
$ omero config append omero.web.ui.right_plugins '["Vitessce", "omero_vitessce/webclient_plugins/right_plugin.vitessce.js.html", "vitessce_tab"]'
$ omero config set omero.web.omero_vitessce.serveraddress '"http://localhost:4080"'
It bundles React in production mode and optimizes the build for the best performance.
See the Create React App section about [deployment](https://facebook.github.io/create-react-app/docs/deployment) for more information.
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"description": "\n\n\nOMERO.omero_vitessce\n=======================\n\nOMERO-vitessce is an OMERO.web plugin for the [Vitessce](http://vitessce.io/) multimodal data viewer. \n\nInstallation\n============\n\nThis section assumes that an OMERO.web is already installed.\n\nInstall the app using [pip](https://pip.pypa.io/en/stable/):\n\nNB: You need to ensure that you are running `pip` from the python environment\nwhere `omero-web` is installed.\n\n $ pip install -U omero-vitessce\n\nAdd the app to the `omero.web.apps` setting:\n\n $ omero config append omero.web.apps '\"omero_vitessce\"'\n\nAdd `omero_vitessce` as a tab in the right-hand-side panel:\n\n $ omero config append omero.web.ui.right_plugins '[\"Vitessce\", \"omero_vitessce/webclient_plugins/right_plugin.vitessce.js.html\", \"vitessce_tab\"]'\n\nAdd `omero_vitessce` as an open-with option:\n\n omero config append omero.web.open_with '[\"omero_vitessce\", \"open_vitessce\", {\"supported_objects\": [\"project\", \"dataset\", \"image\"], \"label\": \"Vitessce\"}]'\n\nAdd the omero web address (replace \u00b4'\"http://localhost:4080\"'\u00b4 with your address):\n\n $ omero config set omero.web.omero_vitessce.serveraddress '\"http://localhost:4080\"'\n \nNow restart OMERO.web as normal for the configuration above to take effect.\n\n### omero-web-zarr\nWhile [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\nomero-web-zarr is necessary to take advantage of the autogenerated config files for the Vitessce viewer,\nas they rely on omero-web-zarr to serve the images to the viewer.\n\nPlease see https://pypi.org/project/omero-web-zarr/ for instructions on installing and enabling the omero-web-zarr plugin.\n\nUsage\n============\n\n### Selecting the viewer\nThe plugin can be used with:\n- `Vitessce` Tab on the right hand side panel.\n- `Open with` `->` `Vitessce` on the left side panel. \n\n#### Right-hand-side panel:\n- **Prexisting config files**:\n\nClicking the link will open a new tab with the viewer displaying the selected configuration. \n\n\n- **Generating custom config files**:\n\nThe form allows the user to automatically generate a config file with the selected parameters. After clicking the `Generate Config` button\na config file is generated and attached to the dataset/image. The viewer displaying the autogenerated configuration will open in a new tab. \n\n\n#### Open-with:\nRight click on a `dataset` or an `images` in the left-panel and select `open-with` -> `Vitessce`. \nThis will open the vitessce viewer in a new tab using the first configuration file attachement.\n\n\n### Viewer window\nAfter autogenerating or selecting a config file, the Vitessce viewer is opened in a new tab:\n\n\nThe viewer panels can also be rearranged to better fit the image type/size.\n\n\n### Config files\nThe omero-vitessce plugin considers all files with the `.json` extension attached to the image or dataset as config files for the viewer.\nThe config files should follow the vitessce view-config-json format: http://vitessce.io/docs/view-config-json/\n\n#### Custom config files generated from the right-tab\nConfig files can be generated for:\n- `images`\n- `datasets`\n\nAssumes that [omero-web-zarr](https://github.com/ome/omero-web-zarr) is available to serve the images.\nThe 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.\nOnly files attached to the dataset/image are available in the form.\n\nThe following fields are available:\n- `Save Config` (required, `True`): Save the viewer configuration as an attahment to the current Image/Dataset before launching the viewer.\n- `Config file name` (optional, \"VitessceConfig-YYYY.MM.DD_HHMMSS.json\"): Name of the config file to attach, a \".json\" extension is added if missing. \t\n- `Images` (required): \t OMERO Image(s) to view, assumes the same pixel size for all images.\n- `Segmentation` (optional, `None`): \t Label image to overlay on the image, pixel values correspond to cell identities.\n- `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.\n- `Cell identities` (optional, `None`): \t `.csv` file / OMERO.table with at least 2 columns: `Cell id column` and `Label column` defined in the 2 fields below. \n- `Cell id column` (optional, \"cell_id\"): \t Name of the `Cell id column` used in `Cell identities`, `Expression`, `Embeddings`.\n- `Label column` (optional, \"label\"): \t Name of the `Label` used in `Cell identities`.\n- `Expression` \t (optional, `None`): `.csv` file / OMERO.table with the `Cell id column` all other columns are considered as expression values and should be numerical.\n- `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. \n- `Embedding x` (optional, \"UMAP_1\"): \t Name of the `Embedding x` used in `Embeddings`.\n- `Embedding y` (optional, \"UMAP_2\"): \t Name of the `Embedding y` used in `Embeddings`.\n- `Molecules` (optional, `None`): \t `.csv` file / OMERO.table with at least 4 columns: Molecule id, label, x, y (headers in the fields below). \n- `Molecule id` (optional, \"id\"): \t Name of the `Molecule id column` used in `Molecules`.\n- `Molecule label` (optional, \"gene\"): \t Name of the `Molecule label column` used in `Molecules`.\n- `Molecule x` (optional, \"x\"): \t Name of the `Molecule x column` used in `Molecules`.\n- `Molecule y` (optional, \"y\"): \t Name of the `Molecule y column` used in `Molecules`.\n- `Histograms` (required , `True`): \t Add 3 plots showing: The number of transcripts per cell, the number of cells in each set, gene expression in each set.\n- `Heatmap` (required , `True`): Adds an heatmap.\n- `Status` (required , `False`): Adds a status panel to display info on the selected cell.\n- `Description` (required , `False`): Adds a description panel to display info on the dataset/image (taken from the description metadata field from OMERO).\n\nThe `Config file name` field depends on the `Save Config` field. When the `Save Config` field is not checked, the `Config file name` field is disabled and its value ignored. \nThe `ROIs` and `Segmentation` fields are mutually exclusive, when the ROI field is selected the segmentation image is not considered. \nThe `Expression` and `Cell identities` files are required to show the histograms. \nThe `Embeddings` file is necessary to show the cells in a scatterplot. \nThe `Molecules` file is used to overlay molecules on the image. All molecules are displayed and selecting by gene is not yet possible. \nThe `Status` panel will be empty unless a `Segmentation` or `Embeddings` are provided. \n\nThe `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.\nThe 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.\n\nOMERO.tables for use with omero-vitessce can be generated with:\n- OMERO python API (https://omero.readthedocs.io/en/stable/developers/Tables.html) or ezomero (https://thejacksonlaboratory.github.io/ezomero/ezomero.html#ezomero.post_table)\n- Fiji (https://wiki-biop.epfl.ch/en/data-management/omero/omero-tables#create-omerotables-from-a-fiji-script)\n- QuPath (https://wiki-biop.epfl.ch/en/data-management/omero/qupath#annotations-measurement-tables)\n- other [tools](https://omero-guides.readthedocs.io/en/latest/external_tools.html) / [APIs](https://omero-guides.readthedocs.io/en/latest/api_usage.html):\n\nOMERO.tables with a number of rows > `omero.web.max_table_download_rows` (default `10000`) will be truncated, and the value ignored by omero-vitessce.\n\n#### Attaching preexisting config files\nCustom config files should have a `.json` extension and added as attachements to a dataset or an image.\nThe configuration files does not need to refer to the dataset / image it is attached to and can refer to other images.\n\nFor how to create a custom config file see:\n- [VItessce Docs](http://vitessce.io/docs/view-config-json/)\n- [Vitessce Examples](http://vitessce.io/examples/)\n\n#### Serving the images / rois / data / metadata\nImages and data can be served through:\n- [omero-web-zarr](https://pypi.org/project/omero-web-zarr/): OME-NGFF images only.\n- [omero-openlink](https://github.com/sukunis/OMERO.openlink): all images and file attachements.\n- `webclient/annotation/` endpoint: only for Annotations (useful for file attachments).\n- `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.\n- `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.\n\nExample showing ROIs from OMERO displayed in the omero-vitessce viewer window:\n\n\nDevelopment\n=======================\n\n## Sources\n\nThe main sources this project relies on are:\n- omero-vitessce from Will Moore for handling ROIs: https://github.com/will-moore/omero-vitessce\n- cookiecutter-omero-webapp: https://github.com/ome/cookiecutter-omero-webapp\n- `react_webapp` from omero-web-apps-examples: https://github.com/ome/omero-web-apps-examples/tree/master/react-webapp\n- Vitessce python package used for generating config files http://python-docs.vitessce.io/\n- omero-web-zarr to serve OME-NGFF images: https://github.com/ome/omero-web-zarr\n- omero-openlink to serve images and other files: https://github.com/sukunis/OMERO.openlink\n- omero-test-infra for testing: https://github.com/ome/omero-test-infra\n\n## Tests\n\n### Test dataset\nThe dataset used for automated testing is at: [test/data/MB266](test/data/MB266)\nThis is a cropped version derived from larger images and their associated data available at:\nhttps://doi.org/10.5281/zenodo.13832665\n\nThe original data are available at:\nhttps://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1093\n\nThe associated publication is available at:\nhttps://www.biorxiv.org/content/10.1101/2024.04.03.586404v1\n\n### omero-test-infra configuration\n[omero-test-infra](https://github.com/ome/omero-test-infra) is used for automated tests with [github-actions](.github/workflows/omero_plugin.yml).\nThe workflow setups an omero installation in docker and then:\n1) Runs [app-config](.omeroci/app-config) to set up the omero-web plugin configuration.\n2) Runs [app-build](.omeroci/app-build) which:\n- runs to create a test user/group and upload a [test dataset](test/data/MB266).\n- runs pytest tests in: [test/integration](test/integration) \n\nIt is possible to perform these tests locally by:\n1) Starting the docker daemon.\n2) Cloning the omero-test infra repository inside the base folder of omero-vitessce: `git clone https://github.com/openmicroscopy/omero-test-infra .omero`\n3) Running: `.omero/app-docker`\n\n## React web app\n\n### omero_vitessce web app\n\nWe serve a custom version of the vitesce app: http://vitessce.io/\n\nThe app sets up a vitessce view configured through a text file in json format: http://vitessce.io/docs/view-config-json/\n\nThe configuration file is taken from the `?config` url parameter.\n\n### Installation\n\nThis project was created with [Create React App](https://github.com/facebook/create-react-app).\n\nYou can run this project in development mode or as an OMERO.web Django app.\n\nTo get started:\n\n $ cd vitessce_app\n $ npm install\n\nIn the project directory, you can run:\n\n### `npm start`\n\nRuns the app in the development mode.<br>\nOpen [http://localhost:3000](http://localhost:3000) to view it in the browser.\n\nThe page will reload if you make edits.<br>\nYou will also see any lint errors in the console.\n\n### `npm run build`\n\nBuilds the app for production to the `build` folder and copies the\nhtml and static files to the Django app in `vitessce app`. See the [deploy_build.sh]() script.<br>\n\nYou also need to install the app into your `omero-web` environment:\n\n # cd to the root of the repo\n $ pip install -e .\n\nYou will need to have the app configured in your OMERO.web install:\n\n $ omero config append omero.web.apps '\"omero_vitessce\"'\n $ omero config append omero.web.ui.right_plugins '[\"Vitessce\", \"omero_vitessce/webclient_plugins/right_plugin.vitessce.js.html\", \"vitessce_tab\"]'\n $ omero config set omero.web.omero_vitessce.serveraddress '\"http://localhost:4080\"'\n\nIt bundles React in production mode and optimizes the build for the best performance.\n\nSee the Create React App section about [deployment](https://facebook.github.io/create-react-app/docs/deployment) for more information.\n",
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