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Update README.md
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@MicheleBortol
MicheleBortol authored Aug 27, 2024
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Expand Up @@ -72,7 +72,7 @@ This will open the vitessce viewer in a new tab using the first configuration fi

### Viewer window
After autogenerating or selecting a config file, the Vitessce viewer is opened in a new tab:
![Viewer GIF](https://github.com/user-attachments/assets/719a3093-2a6a-480d-afc9-522b4873310e)
![Viewer GIF](https://github.com/user-attachments/assets/0f1effac-e681-4782-a69e-76702451fcbb)



Expand All @@ -91,25 +91,25 @@ 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.
`Image` (required): OMERO Image to view, OME-NGFF images only.
`Segmentation` (optional, `None`): Segmentation to overlay on the image, OME-NGFF images only.
`Cell identities` (optional, `None`): `.csv` file with at least 2 columns: `Cell id column` and `Label column` defined in the 2 fileds 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 fileds 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).
`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 .
- `Config file name` (required, "VitessceConfig-YYYY.MM.DD_HHMMSS.json"): Name of the config file to attach, a ".json" extension is added if missing.
- `Image` (required): OMERO Image to view, OME-NGFF images only.
- `Segmentation` (optional, `None`): Segmentation to overlay on the image, OME-NGFF images only.
- `Cell identities` (optional, `None`): `.csv` file with at least 2 columns: `Cell id column` and `Label column` defined in the 2 fileds 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 fileds 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).
- `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 `Expression` and `Cell identities` files are required to show the histograms.
The `Embeddings` file is necessary to show the cells in a scatterplot.
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