Update README.md

Author: MicheleBortol

README.md

@@ -53,14 +53,15 @@ The plugin can be used with:
 - `Open with` `->` `Vitessce` on the left side panel. 
 
 #### Right-hand-side panel:
-- **Prexisting config files**:  
-![Link-List-image](https://github.com/user-attachments/assets/b95c77a3-77c5-4221-83f2-c9c460a83f2e)  
-Clicking the link will open a new tab with the viewer displaying the selected configuration.
-
-- **Autogenerating config file**:  
-![Form-image](https://github.com/user-attachments/assets/5c81aba3-adfd-465c-86f0-9e03506ec3ea)  
-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.  
+- **Prexisting config files**:
+  Clicking the link will open a new tab with the viewer displaying the selected configuration.  
+  ![Link-List-image](https://github.com/user-attachments/assets/b95c77a3-77c5-4221-83f2-c9c460a83f2e)  
+
+
+- **Autogenerating config file**:
+  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/5c81aba3-adfd-465c-86f0-9e03506ec3ea)  
 
 #### Open-with:
 Right click on a `dataset` or an `images` in the left-panel and select `open-with` -> `Vitessce`.  
@@ -74,7 +75,7 @@ After autogenerating or selecting a config file, the Vitessce viewer is opened i
 
 
 ### Config files
-The omero-vitessce plugin considers all files with the `.json.txt` extension attached to the image or dataset as config files for the viewer.
+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/
 
 #### Autogenerated config files
@@ -84,12 +85,29 @@ Config files can be autogenerated for:
 
 Assumes that the images are in the OME-NGFF format v0.4 and that [omero-web-zarr](https://github.com/ome/omero-web-zarr) is
 available to serve the images.
+The attachements must be 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:
+`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`.
+`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.
+
+The `Expression` and `Cell identities` files are required to show the histograms.  
+The `Embeddings` file is necessary to show the cells in a scatterplot.
 
 #### Custom config files
-Custom config files should have a `.json.txt` extension and added as attachements to a dataset or an image.
+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.
-
-
 [examples](http://vitessce.io/examples/)
 
 #### Serving the images / data /metadata