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Update README.md
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MicheleBortol authored Aug 16, 2024
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Expand Up @@ -54,19 +54,21 @@ The plugin can be used with:

#### Right-hand-side panel:
- **Prexisting config files**:
![Right-Config](https://github.com/user-attachments/assets/b8fea5f0-1d8f-4578-a577-8744d32dcaa5)

Clicking the link will open a new tab with the viewer displaying the selected configuration.

- **Autogenerating config file**:
![Right-Auto](https://github.com/user-attachments/assets/8dfa22cc-dbb5-493d-b837-d609a11a1346)
Clicking the button will autogenerate a config file and attach it to the dataset/image, and the viewer displaying the autogenerated configuration.
![image](https://github.com/user-attachments/assets/c8450916-aceb-4036-a23b-580094c207ed)
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.

#### Open-with:
Right click on a `dataset` or an `images` in the left-panel and select `open-with` -> `Vitessce`.
This will open the vitessce viewer in a new tab using the first configuration file attachement.
![Openwith-image](https://github.com/user-attachments/assets/f75cc27c-4cd3-4a19-ae20-7d8f0a47aa87)

### Viewer window
After using a The Vitessce viewer is opened in a new tab:
After autogenerating or selecting a config file, rhe Vitessce viewer is opened in a new tab:
![image](https://github.com/user-attachments/assets/77de517e-67e4-42d6-a2b6-2a3a6a11dc7e)

### Config files
Expand All @@ -75,8 +77,8 @@ The config files should follow the vitessce view-config-json format: http://vite

#### Autogenerated config files
Config files can be autogenerated for:
- `images`: A spatial view and a layer controller view are setup for the image.
- `datasets`: All images in the dataset are bundled togheter and a spatial view and a layer controller are setup.
- `images`
- `datasets`

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.
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