From 3bb7179860c4d5ad70adae6c29263d0562474e0f Mon Sep 17 00:00:00 2001 From: Michele Bortolomeazzi Date: Thu, 5 Sep 2024 13:34:23 +0200 Subject: [PATCH 1/3] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index ea83225..e102bc4 100644 --- a/README.md +++ b/README.md @@ -91,7 +91,7 @@ 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. +- `Image` (required): OMERO Image to view. - `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`. From 1a3f071942e0f8f9967945c2bb5b8c10861c597a Mon Sep 17 00:00:00 2001 From: Michele Bortolomeazzi Date: Thu, 5 Sep 2024 13:35:42 +0200 Subject: [PATCH 2/3] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e102bc4..1a923f8 100644 --- a/README.md +++ b/README.md @@ -92,7 +92,7 @@ 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. -- `Segmentation` (optional, `None`): Segmentation to overlay on the image, OME-NGFF images only. +- `Segmentation` (optional, `None`): Label image to overlay on the image, pixel values correspond to cell identities. - `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`. From d9655fbb0f3598b541e40c9fda602220d8827943 Mon Sep 17 00:00:00 2001 From: Michele Bortolomeazzi Date: Thu, 5 Sep 2024 15:00:07 +0200 Subject: [PATCH 3/3] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 1a923f8..a201337 100644 --- a/README.md +++ b/README.md @@ -93,11 +93,11 @@ 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. - `Segmentation` (optional, `None`): Label image to overlay on the image, pixel values correspond to cell identities. -- `Cell identities` (optional, `None`): `.csv` file with at least 2 columns: `Cell id column` and `Label column` defined in the 2 fileds below. +- `Cell identities` (optional, `None`): `.csv` file 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 fileds below. +- `Embeddings` (optional, `None`): `.csv` file 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).