Merge pull request #11 from NFDI4BIOIMAGE/dev

Support OMERO ROIs as cell segmentation.

README.md

@@ -64,9 +64,8 @@ Clicking the link will open a new tab with the viewer displaying the selected co
 
 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/94727eb5-486c-4d9f-beae-b7559224ddfd)
+![Form-image](https://github.com/user-attachments/assets/0c6513e4-1f8f-40b0-b919-e1c9d57c2190)
 
-
 #### 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.
@@ -95,6 +94,7 @@ 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. 	
 - `Images`               (required): 	                                       OMERO Image(s) to view, assumes the same pixel size for all images.
 - `Segmentation`        (optional, `None`): 	                               Label image to overlay on the image, pixel values correspond to cell identities.
+- `ROIs`                (optional, `False`):                                   Use the ROIs from OMERO as a cell segmentation. Assumes 1 polygon shape per ROI, whose text value is the cell identity.
 - `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`.
@@ -112,6 +112,7 @@ The following fields are available:
 - `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 `ROIs` and `Segmentation` fields are mutually exclusive, when the ROI field is selected the segmentation image is not considered.
 The `Expression` and `Cell identities` files are required to show the histograms.  
 The `Embeddings` file is necessary to show the cells in a scatterplot.
 The `Molecules` file is used to overlay molecules on the image. All molecules are displayed and selecting by gene is not yet possible.  
@@ -125,19 +126,24 @@ For how to create a custom config file see:
 - [VItessce Docs](http://vitessce.io/docs/view-config-json/)
 - [Vitessce Examples](http://vitessce.io/examples/)
 
-#### Serving the images / data /metadata
+#### Serving the images / rois / data / metadata
 Images and data can be served through:
 - [omero-web-zarr](https://pypi.org/project/omero-web-zarr/):  OME-NGFF images only.
 - [omero-openlink](https://github.com/sukunis/OMERO.openlink): all images and file attachements.
 - `webclient/annotation/` endpoint: only for Annotations (useful for file attachments).
+- `omero_vitessce/vitessce_json_rois/ID1,ID2,...` endpoint where `ID1,ID2,...` is a comma-separated list of image ids.
+
+Example showing ROIs from OMERO displayed in the omero-vitessce viewer window:
+![image](https://github.com/user-attachments/assets/223072d6-9aa7-4b96-a199-65bbab863c1b)
+
 
 Development
 =======================
 
 ## Sources
 
 The main sources this project relies on are:
-- omero-vitessce from Will Moore: https://github.com/will-moore/omero-vitessce
+- omero-vitessce from Will Moore for handling ROIs: https://github.com/will-moore/omero-vitessce
 - cookiecutter-omero-webapp: https://github.com/ome/cookiecutter-omero-webapp
 - `react_webapp` from omero-web-apps-examples: https://github.com/ome/omero-web-apps-examples/tree/master/react-webapp
 - Vitessce python package used for generating config files http://python-docs.vitessce.io/

omero_vitessce/forms.py

@@ -25,6 +25,7 @@ class ConfigForm(forms.Form):
     images_help = "OMERO Image(s) to view, assumes identical pixel size."
     segmentation_help = "Label image to overlay on the image, \
             pixel values should correspond to cell identities."
+    rois_help = "Use image ROIs as segmentation."
     cell_identities_help = ".csv file with at least 2 columns: \
             Cell id column and Label column defined in the 2 fields below."
     cell_id_help = "Name of the Cell id column used in \
@@ -78,6 +79,14 @@ def __init__(self, file_names, file_urls,
         self.fields["segmentation"] = forms.ChoiceField(
                 choices=self.image_choices, required=False,
                 help_text=ConfigForm.segmentation_help)
+        # Segmentation and rois are mutually exclusive,
+        # Setting rois to true disables the segmentation
+        self.fields["rois"] = forms.BooleanField(
+                initial=False, required=False,
+                help_text=ConfigForm.rois_help)
+        self.fields["rois"].widget.attrs = \
+            {"onclick":
+             "javascript:toggleDisabled('id_rois', 'id_segmentation', true);"}
 
         self.fields["cell_identities"] = forms.ChoiceField(
                 choices=self.text_choices, required=False,

omero_vitessce/templates/omero_vitessce/vitessce_open_with.html

@@ -76,6 +76,12 @@
 						</div></th>
 						<th style="text-align:left;">{{ form.segmentation }}</th>
 					</tr>
+					<tr style="height:2vh">
+						<th><div class="tooltip">{{ form.rois.label_tag }}
+							<span class="tooltiptext">{{ form.rois.help_text }}</span>
+						</div></th>
+						<th style="text-align:left;">{{ form.rois }}</th>
+					</tr>
 					<tr style="height:2vh">
 						<th><div class="tooltip">{{ form.cell_identities.label_tag }}
 							<span class="tooltiptext">{{ form.cell_identities.help_text }}</span>
@@ -183,6 +189,24 @@
 					</table>
 					<input type = "submit" value = "Generate Config"> 
 				</form>
+				<script>
+					function toggleDisabled(divId1, divId2, value) {
+						   const field_to_check = document.getElementById(divId1);
+						   const field_to_disable = document.getElementById(divId2);
+						   if (field_to_check.value === value || field_to_check.checked == value) {
+							   field_to_disable.disabled = true;
+						   }
+						   else {
+							   field_to_disable.disabled = false;
+						   }
+					}
+				</script>
+				<script>
+					// Ensure checkbox is unchecked when the page loads
+					window.onload = function() {
+					    document.getElementById('id_rois').checked = false;
+					};
+				</script>
 			{% else %}
 				<p style="font-size:medium%"> Autogenerating config files requires the 
 				<a  href=https://github.com/ome/omero-web-zarr target="_blank">omero-web-zarr</a>

omero_vitessce/templates/omero_vitessce/vitessce_panel.html

@@ -76,6 +76,12 @@
 						</div></th>
 						<th style="text-align:left;">{{ form.segmentation }}</th>
 					</tr>
+					<tr>
+						<th><div class="tooltip">{{ form.rois.label_tag }}
+							<span class="tooltiptext">{{ form.rois.help_text }}</span>
+						</div></th>
+						<th style="text-align:left;">{{ form.rois }}</th>
+					</tr>
 					<tr>
 						<th><div class="tooltip">{{ form.cell_identities.label_tag }}
 							<span class="tooltiptext">{{ form.cell_identities.help_text }}</span>
@@ -183,6 +189,18 @@
 					</table>
 					<input type = "submit" value = "Generate Config"> 
 				</form>
+				<script>
+					function toggleDisabled(divId1, divId2, value) {
+						   const field_to_check = document.getElementById(divId1);
+						   const field_to_disable = document.getElementById(divId2);
+						   if (field_to_check.value === value || field_to_check.checked == value) {
+							   field_to_disable.disabled = true;
+						   }
+						   else {
+							   field_to_disable.disabled = false;
+						   }
+					}
+				</script>
 			{% else %}
 				<p> Autogenerating config files requires the 
 				<a  href=https://github.com/ome/omero-web-zarr target="_blank">omero-web-zarr</a>

omero_vitessce/urls.py

@@ -11,6 +11,10 @@
     re_path(r"^generate_config$", views.vitessce_index,
             name="generate_config"),
 
+    # json response with ROIs
+    re_path(r"vitessce_json_rois/(?P<img_ids>[0-9,]+)",
+            views.vitessce_json_rois, name="vitessce_rois"),
+
     # Right panel plugin
     re_path(r"(?P<obj_type>[a-z]+)/(?P<obj_id>[0-9]+)",
             views.vitessce_panel, name='vitessce_tab'),

omero_vitessce/utils.py

@@ -1,5 +1,7 @@
 import json
 from pathlib import Path
+from shapely.geometry import Polygon
+from omero_marshal import get_encoder
 
 from omero.util.temp_files import create_path
 
@@ -18,7 +20,7 @@ def get_files_images(obj_type, obj_id, conn):
     """ Gets all the non config files attached to an object,
     and images if the object is a dataset,
     and returns a list of file names and a list of urls
-    for the files and eventually the images.
+    for the files and eventually the images, plus the image ids.
     """
     obj = conn.getObject(obj_type, obj_id)
     file_names = [
@@ -29,17 +31,19 @@ def get_files_images(obj_type, obj_id, conn):
                   if i.getFileName().endswith(".csv")]
     file_urls = [i.getId() for i in file_names]
     file_names = [i.getFileName() for i in file_names]
-    file_urls = [SERVER + "/webclient/annotation/" + str(i) for i in file_urls]
+    file_urls = [build_attachement_url(i) for i in file_urls]
 
     if obj_type == "dataset":
         imgs = list(obj.listChildren())
-        img_urls = [build_zarr_image_url(i.getId()) for i in imgs]
+        img_ids = [i.getId() for i in imgs]
+        img_urls = [build_zarr_image_url(i) for i in img_ids]
         img_names = [i.getName() for i in imgs]
     else:
         img_urls = [build_zarr_image_url(obj_id)]
         img_names = [obj.getName()]
+        img_ids = [obj_id]
 
-    return file_names, file_urls, img_names, img_urls
+    return file_names, file_urls, img_names, img_urls, img_ids
 
 
 def build_viewer_url(config_id):
@@ -57,6 +61,13 @@ def build_zarr_image_url(image_id):
     return SERVER + "/zarr/v0.4/image/" + str(image_id) + ".zarr"
 
 
+def build_attachement_url(obj_id):
+    """ Generates urls like:
+    http://localhost:4080/webclient/annotation/99999
+    """
+    return SERVER + "/webclient/annotation/" + str(obj_id)
+
+
 def get_attached_configs(obj_type, obj_id, conn):
     """ Gets all the ".json" files attached to an object
     and returns a list of file names and a list of urls
@@ -144,6 +155,71 @@ def add_cell_identities(config_args, vc_dataset):
     return vc_dataset
 
 
+class VitessceShape():
+    """
+    Converts an OMERO ROI shape to a vitessce compatibel represetnation
+    https://github.com/will-moore/omero-vitessce/blob/master/omero_vitessce/views.py
+    """
+    def __init__(self, shape):
+        self.shape = self.to_shapely(shape)
+        self.name = shape.getTextValue().getValue()
+
+    def to_shapely(self, omero_shape):
+        encoder = get_encoder(omero_shape.__class__)
+        shape_json = encoder.encode(omero_shape)
+
+        if "Points" in shape_json:
+            xy = shape_json["Points"].split(" ")
+            coords = []
+            for coord in xy:
+                c = coord.split(",")
+                coords.append((float(c[0]), float(c[1])))
+            return Polygon(coords)
+
+    def poly(self):
+        # Use 2 to get e.g. 8 points from 56.
+        return list(self.shape.simplify(2).exterior.coords)
+
+
+def process_rois(img_ids, conn):
+    """
+    Generates shapely polygons from OMERO rois,
+    extracted from a list of images
+    """
+    rois = []
+    for img_id in img_ids:
+        img = conn.getObject("Image", img_id)
+        if not img:
+            continue
+        rois += img.getROIs()
+    shapes = [VitessceShape(r.getShape(0)) for r in rois]
+    return shapes
+
+
+def make_cell_json(shapes):
+    """
+    Turns a list of polygons into a dictionary:
+    {cell_id: [[x, y], ...]}
+    """
+    cell_dict = {}
+    for s in shapes:
+        cell_dict[s.name] = s.poly()
+    return cell_dict
+
+
+def add_rois(img_ids, vc_dataset, conn):
+    """
+    Adds a url to the rois in json format to the vitessce config
+    """
+    cell_json_url = SERVER + "/omero_vitessce/vitessce_json_rois/" + \
+        ",".join([str(i) for i in img_ids])
+    vc_dataset = vc_dataset.add_file(
+        url=cell_json_url,
+        file_type=Ft.OBS_SEGMENTATIONS_JSON,
+        coordination_values={"obsType": "cell"})
+    return vc_dataset
+
+
 def create_config(config_args, obj_type, obj_id, conn):
     """
     Generates a Vitessce config and returns it,
@@ -154,7 +230,7 @@ def create_config(config_args, obj_type, obj_id, conn):
     # plugin is loaded and the form is submitted then it will not be found
     # and will not be present in the cleaned_data -> None
 
-    file_names, file_urls, img_files, img_urls = get_files_images(
+    file_names, file_urls, img_files, img_urls, img_ids = get_files_images(
         obj_type, obj_id, conn)
     config_args = ConfigForm(data=config_args, file_names=file_names,
                              file_urls=file_urls, img_names=img_files,
@@ -212,6 +288,11 @@ def create_config(config_args, obj_type, obj_id, conn):
                 img_url=config_args.get("segmentation"),
                 name="Segmentation", is_bitmask=True)
         images.append(segmentation)
+    if config_args.get("rois"):
+        vc_dataset = add_rois(img_ids, vc_dataset, conn)
+        vc.link_views([sp, lc], ["spatialSegmentationLayer"],
+                      [{"opacity": 1, "radius": 0,
+                        "visible": True, "stroked": False}])
     if config_args.get("molecules"):
         vc_dataset = add_molecules(config_args, vc_dataset)
         vc.link_views([sp, lc], c_types=[Ct.SPATIAL_POINT_LAYER],
@@ -228,7 +309,7 @@ def create_config(config_args, obj_type, obj_id, conn):
     vc.add_coordination_by_dict({
         Ct.SPATIAL_ZOOM: 2,
         Ct.SPATIAL_TARGET_X: 0,
-        Ct.SPATIAL_TARGET_Y: 0
+        Ct.SPATIAL_TARGET_Y: 0,
     })
 
     displays = hconcat(*displays)
@@ -241,10 +322,20 @@ def create_config(config_args, obj_type, obj_id, conn):
         controllers = hconcat(controllers, hists)
     vc.layout(vconcat(displays, controllers))
 
-    return vc
+    vc_dict = vc.to_dict()
+
+    # OBS_SEGMENTATIONS_JSON does not work with raster.json
+    # https://github.com/vitessce/vitessce/discussions/1962
+    if config_args.get("rois"):
+        for d in vc_dict["datasets"]:
+            for f in d["files"]:
+                if f["fileType"] == "raster.json":
+                    f["fileType"] = "image.raster.json"
+
+    return vc_dict
 
 
-def attach_config(vc, obj_type, obj_id, filename, conn):
+def attach_config(vc_dict, obj_type, obj_id, filename, conn):
     """
     Generates a Vitessce config for an OMERO image and returns it.
     Assumes the images is an OME NGFF v0.4 file
@@ -257,7 +348,7 @@ def attach_config(vc, obj_type, obj_id, filename, conn):
 
     config_path = Path(config_path).joinpath(filename)
     with open(config_path, "w") as outfile:
-        json.dump(vc.to_dict(), outfile, indent=4, sort_keys=False)
+        json.dump(vc_dict, outfile, indent=4, sort_keys=False)
 
     file_ann = conn.createFileAnnfromLocalFile(
         config_path, mimetype="text/plain")

omero_vitessce/views.py

@@ -1,11 +1,12 @@
 from django.shortcuts import render
-from django.http import HttpResponseRedirect
+from django.http import HttpResponseRedirect, JsonResponse
 
 from omeroweb.webclient.decorators import login_required
 
 from .forms import ConfigForm
 from .utils import get_attached_configs, create_config, attach_config
 from .utils import get_files_images, build_viewer_url
+from .utils import process_rois, make_cell_json
 
 from omeroweb.settings import ADDITIONAL_APPS
 
@@ -36,7 +37,7 @@ def vitessce_panel(request, obj_type, obj_id, conn=None, **kwargs):
                "obj_type": obj_type, "obj_id": obj_id}
 
     if OMERO_WEB_ZARR:
-        files, urls, img_files, img_urls = get_files_images(
+        files, urls, img_files, img_urls, _ = get_files_images(
                 obj_type, obj_id, conn)
         form = ConfigForm(file_names=files, file_urls=urls,
                           img_names=img_files, img_urls=img_urls)
@@ -64,6 +65,17 @@ def generate_config(request, obj_type, obj_id, conn=None, **kwargs):
     return HttpResponseRedirect(viewer_url)
 
 
+@login_required()
+def vitessce_json_rois(request, img_ids, conn=None, **kwargs):
+    """Generate a json response with the polygon coordinates of the
+    vertices of the ROIs on the given images.
+    """
+    img_ids = [int(img_id) for img_id in img_ids.split(",")]
+    shapes = process_rois(img_ids, conn)
+    cell_dict = make_cell_json(shapes)
+    return JsonResponse(cell_dict)
+
+
 @login_required()
 def vitessce_open(request, conn=None, **kwargs):
     """Get the first .json attachement and generate a link for it
@@ -85,7 +97,7 @@ def vitessce_open(request, conn=None, **kwargs):
         context = {"json_configs": dict(),
                    "obj_type": obj_type, "obj_id": obj_id}
     if OMERO_WEB_ZARR:
-        files, urls, img_files, img_urls = get_files_images(
+        files, urls, img_files, img_urls, _ = get_files_images(
                 obj_type, obj_id, conn)
         form = ConfigForm(file_names=files, file_urls=urls,
                           img_names=img_files, img_urls=img_urls)

requirements.txt

@@ -1 +1,2 @@
 vitessce==3.3.0
+shapely==2.0.6