Merge pull request #16 from NFDI4BIOIMAGE/dev

Dev
NFDI4BIOIMAGE · Nov 18, 2024 · 25451eb · 25451eb
2 parents decac5e + 17cd2ec
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diff --git a/README.md b/README.md
@@ -1,7 +1,6 @@
 ![Badge_OMERO](https://github.com/MicheleBortol/omero-vitessce/actions/workflows/omero_plugin.yml/badge.svg)
 ![Badge_PyPI](https://img.shields.io/pypi/v/omero-vitessce?label=pypi%20package)
 
-
 OMERO.omero_vitessce
 =======================
 
@@ -58,15 +57,12 @@ The plugin can be used with:
 Clicking the link will open a new tab with the viewer displaying the selected configuration.  
 ![Link-List-image](https://github.com/user-attachments/assets/7f556f86-7edf-49a0-bf2a-9c5f168922b1)
 
-
-
 - **Generating custom config files**:
 
 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/6e9bbb79-6b40-4d5f-bb0f-48f7bc6a13f1)
 
-
 #### 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.
@@ -76,7 +72,8 @@ This will open the vitessce viewer in a new tab using the first configuration fi
 After autogenerating or selecting a config file, the Vitessce viewer is opened in a new tab:
 ![Viewer GIF](https://github.com/user-attachments/assets/0f1effac-e681-4782-a69e-76702451fcbb)
 
-
+The viewer panels can also be rearranged to better fit the image type/size.
+![Viewer slide](https://github.com/user-attachments/assets/5c8c9559-ea2c-44c9-acbe-26caaf951432)
 
 ### Config files
 The omero-vitessce plugin considers all files with the `.json` extension attached to the image or dataset as config files for the viewer.
@@ -149,8 +146,7 @@ Images and data can be served through:
 - `omero_vitessce/vitessce_json_rois/ID1,ID2,...` endpoint where `ID1,ID2,...` is a comma-separated list of image ids, to get the first shape of each ROI in `json` format.
 
 Example showing ROIs from OMERO displayed in the omero-vitessce viewer window:
-![image](https://github.com/user-attachments/assets/223072d6-9aa7-4b96-a199-65bbab863c1b)
-
+![ROI comparison](https://github.com/user-attachments/assets/807026b8-4ed2-4977-890b-73aa9c547ca2)
 
 Development
 =======================
@@ -223,7 +219,6 @@ Open [http://localhost:3000](http://localhost:3000) to view it in the browser.
 The page will reload if you make edits.<br>
 You will also see any lint errors in the console.
 
-
 ### `npm run build`
 
 Builds the app for production to the `build` folder and copies the
@@ -243,4 +238,3 @@ You will need to have the app configured in your OMERO.web install:
 It bundles React in production mode and optimizes the build for the best performance.
 
 See the Create React App section about [deployment](https://facebook.github.io/create-react-app/docs/deployment) for more information.
-
diff --git a/omero_vitessce/utils.py b/omero_vitessce/utils.py
@@ -309,9 +309,9 @@ def create_config(config_args, obj_type, obj_id, conn):
 
     # Collects the images
     images = []
-    img_urls = config_args.get("images")
-    for n, img_url in enumerate(img_urls):
-        images.append(OmeZarrWrapper(img_url=img_url, name=f"Image {n}"))
+    for img_url in config_args.get("images"):
+        img_file = img_files[img_urls.index(img_url)]
+        images.append(OmeZarrWrapper(img_url=img_url, name=img_file))
 
     sp = vc.add_view(Vt.SPATIAL, dataset=vc_dataset)
     lc = vc.add_view(Vt.LAYER_CONTROLLER, dataset=vc_dataset)
@@ -349,9 +349,11 @@ def create_config(config_args, obj_type, obj_id, conn):
             hm = vc.add_view(Vt.HEATMAP, dataset=vc_dataset)
             displays.append(hm)
     if config_args.get("segmentation"):
+        seg_url = config_args.get("segmentation")
+        seg_name = img_files[img_urls.index(seg_url)]
         segmentation = OmeZarrWrapper(
-                img_url=config_args.get("segmentation"),
-                name="Segmentation", is_bitmask=True)
+                img_url=seg_url, name=seg_name,
+                is_bitmask=True)
         images.append(segmentation)
     if config_args.get("rois"):
         vc_dataset = add_rois(img_ids, vc_dataset, conn)

diff --git a/setup.py b/setup.py
@@ -2,7 +2,7 @@
 
 setup(
     name="omero-vitessce",
-    version="1.2.0",
+    version="1.2.1",
     description="OMERO Vitessce multimodal data viewer plugin for OMERO.web",
     long_description=open('README.md').read(),
     long_description_content_type='text/markdown',

diff --git a/test/data/MB266/VitessceConfig.json b/test/data/MB266/VitessceConfig.json
@@ -74,12 +74,12 @@
                         "usePhysicalSizeScaling": true,
                         "images": [
                             {
-                                "name": "Image 0",
+                                "name": "MB266-DAPI.tiff",
                                 "type": "ome-zarr",
                                 "url": "http://localhost:4080/zarr/v0.4/image/1.zarr"
                             },
                             {
-                                "name": "Segmentation",
+                                "name": "MB266-CELLS.png",
                                 "type": "ome-zarr",
                                 "url": "http://localhost:4080/zarr/v0.4/image/2.zarr",
                                 "metadata": {
@@ -88,8 +88,8 @@
                             }
                         ],
                         "renderLayers": [
-                            "Image 0",
-                            "Segmentation"
+                            "MB266-DAPI.tiff",
+                            "MB266-CELLS.png"
                         ]
                     }
                 }