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Update README.md
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MicheleBortol authored Oct 30, 2024
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Expand Up @@ -64,7 +64,8 @@ Clicking the link will open a new tab with the viewer displaying the selected co

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.
![Form-image](https://github.com/user-attachments/assets/0c6513e4-1f8f-40b0-b919-e1c9d57c2190)
![Form-image](https://github.com/user-attachments/assets/6e9bbb79-6b40-4d5f-bb0f-48f7bc6a13f1)


#### Open-with:
Right click on a `dataset` or an `images` in the left-panel and select `open-with` -> `Vitessce`.
Expand All @@ -91,7 +92,8 @@ The attachements must be in `.csv` format and the column with the cell identifie
Only files attached to the dataset/image are available in the form.

The following fields are available:
- `Config file name` (required, "VitessceConfig-YYYY.MM.DD_HHMMSS.json"): Name of the config file to attach, a ".json" extension is added if missing.
- `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 shape per ROI, whose text value is the cell identity.
Expand All @@ -112,9 +114,10 @@ The following fields are available:
- `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 `ROIs` and `Segmentation` fields are mutually exclusive, when the ROI field is selected the segmentation image is not considered.
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 `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.

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