From 91116860fac8de877e96887313dad6ae38872fb5 Mon Sep 17 00:00:00 2001 From: Michele Bortolomeazzi Date: Tue, 27 Aug 2024 12:51:48 +0200 Subject: [PATCH] Update README.md --- README.md | 40 ++++++++++++++++++++-------------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/README.md b/README.md index 70f7280..c25b1a7 100644 --- a/README.md +++ b/README.md @@ -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) @@ -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.