fractal-analytics-platform · tcompa · Jun 16, 2023 · May 15, 2023 · May 15, 2023 · Jun 12, 2023
diff --git a/examples/00_user_setup/install_client.sh b/examples/00_user_setup/install_client.sh
@@ -1,4 +1,4 @@
-VERSION="1.2.0"
+VERSION="1.3.0a3"
 
 ENVNAME=fractal-client-$VERSION
 conda deactivate

diff --git a/examples/00_user_setup/local_user_setup.sh b/examples/00_user_setup/local_user_setup.sh
@@ -21,4 +21,4 @@ FRACTAL_SERVER=http://localhost:$PORT
 fractal user whoami
 
 # Trigger collection of core tasks
-fractal task collect fractal-tasks-core --package-version 0.9.4
+fractal task collect fractal-tasks-core --package-version 0.10.0a4 --package-extras fractal-tasks
diff --git a/examples/00_user_setup/setup_multi_user.sh b/examples/00_user_setup/setup_multi_user.sh
@@ -38,4 +38,4 @@ FRACTAL_SERVER=http://localhost:$PORT
 fractal user whoami
 
 # Trigger collection of core tasks
-fractal task collect fractal-tasks-core --package-version 0.9.4
+fractal task collect fractal-tasks-core --package-version 0.10.0a4 --package-extras fractal-tasks
diff --git a/examples/01_cardio_tiny_dataset/Parameters/.gitignore b/examples/01_cardio_tiny_dataset/Parameters/.gitignore
@@ -1 +0,0 @@
-args_measurement.json

diff --git a/examples/01_cardio_tiny_dataset/Parameters/args_cellpose_segmentation.json b/examples/01_cardio_tiny_dataset/Parameters/args_cellpose_segmentation.json
@@ -1,6 +1,8 @@
 {
     "level": 2, 
-    "wavelength_id": "A01_C01", 
+    "channel":{
+        "wavelength_id": "A01_C01"
+    }, 
     "output_label_name": "nuclei", 
     "input_ROI_table": "well_ROI_table",
     "model_type": "nuclei",

diff --git a/examples/01_cardio_tiny_dataset/Parameters/args_create_ome_zarr.json b/examples/01_cardio_tiny_dataset/Parameters/args_create_ome_zarr.json
@@ -1,25 +1,31 @@
 {
     "allowed_channels": [
         {
-            "colormap": "00FFFF",
+            "color": "00FFFF",
             "wavelength_id": "A01_C01",
-            "end": 800,
             "label": "DAPI",
-            "start": 110
+            "window":{
+                "start": 110,
+                "end": 800
+            }
         },
         {
-            "colormap": "FF00FF",
-            "end": 290,
+            "color": "FF00FF",
             "wavelength_id": "A01_C02",
             "label": "nanog",
-            "start": 110
+            "window": {
+                "start": 110,
+                "end": 290
+            }
         },
         {
-            "colormap": "FFFF00",
-            "end": 1600,
+            "color": "FFFF00",
             "wavelength_id": "A02_C03",
             "label": "Lamin B1",
-            "start": 110
+            "window": {
+                "start": 110,
+                "end": 1600
+            }
         }
         ]
     ,

diff --git a/examples/01_cardio_tiny_dataset/Parameters/args_measurement.json b/examples/01_cardio_tiny_dataset/Parameters/args_measurement.json
@@ -0,0 +1,23 @@
+{
+  "level": 0,
+  "input_ROI_table": "well_ROI_table",
+  "workflow_file": "/home/tommaso/Fractal/fractal-demos/examples/01_cardio_tiny_dataset/regionprops_from_existing_labels_feature.yaml",
+  "input_specs": {
+    "dapi_img": {
+      "type": "image",
+      "channel":{
+                "wavelength_id": "A01_C01"
+      }
+    },
+    "label_img": {
+      "type": "label",
+      "label_name": "nuclei"
+    }
+  },
+  "output_specs": {
+    "regionprops_DAPI": {
+      "type": "dataframe",
+      "table_name": "nuclei"
+    }
+  }
+}
diff --git a/examples/01_cardio_tiny_dataset/run_example.sh b/examples/01_cardio_tiny_dataset/run_example.sh
@@ -1,4 +1,4 @@
-LABEL="cardiac-test-4"
+LABEL="cardiac-test-3"
 
 ###############################################################################
 # IMPORTANT: This defines the location of input & output data
@@ -49,13 +49,12 @@ echo "WF_ID: $WF_ID"
 ###############################################################################
 
 # Add tasks to workflow
-fractal --batch workflow add-task $WF_ID "Create OME-Zarr structure" --args-file Parameters/args_create_ome_zarr.json --meta-file Parameters/example_meta.json
-fractal --batch workflow add-task $WF_ID "Convert Yokogawa to OME-Zarr"
-fractal --batch workflow add-task $WF_ID "Copy OME-Zarr structure"
-fractal --batch workflow add-task $WF_ID "Maximum Intensity Projection"
-fractal --batch workflow add-task $WF_ID "Cellpose Segmentation" --args-file Parameters/args_cellpose_segmentation.json #--meta-file Parameters/cellpose_meta.json
-echo "{\"level\": 0, \"input_ROI_table\": \"well_ROI_table\", \"workflow_file\": \"`pwd`/regionprops_from_existing_labels_feature.yaml\", \"input_specs\": {\"dapi_img\": {\"type\": \"image\", \"wavelength_id\": \"A01_C01\"}, \"label_img\": {\"type\": \"label\", \"label_name\": \"nuclei\"}}, \"output_specs\": {\"regionprops_DAPI\": {\"type\": \"dataframe\",\"table_name\": \"nuclei\"}}}" > Parameters/args_measurement.json
-fractal --batch workflow add-task $WF_ID "Napari workflows wrapper" --args-file Parameters/args_measurement.json --meta-file Parameters/example_meta.json
+fractal --batch workflow add-task $PRJ_ID $WF_ID --task-name "Create OME-Zarr structure" --args-file Parameters/args_create_ome_zarr.json --meta-file Parameters/example_meta.json
+fractal --batch workflow add-task $PRJ_ID $WF_ID --task-name "Convert Yokogawa to OME-Zarr"
+fractal --batch workflow add-task $PRJ_ID $WF_ID --task-name "Copy OME-Zarr structure"
+fractal --batch workflow add-task $PRJ_ID $WF_ID --task-name "Maximum Intensity Projection"
+fractal --batch workflow add-task $PRJ_ID $WF_ID --task-name "Cellpose Segmentation" --args-file Parameters/args_cellpose_segmentation.json #--meta-file Parameters/cellpose_meta.json
+fractal --batch workflow add-task $PRJ_ID $WF_ID --task-name "Napari workflows wrapper" --args-file Parameters/args_measurement.json --meta-file Parameters/example_meta.json
 
 # Apply workflow
-fractal workflow apply -o $DS_OUT_ID -p $PRJ_ID $WF_ID $DS_IN_ID
+fractal workflow apply $PRJ_ID $WF_ID $DS_IN_ID $DS_OUT_ID
diff --git a/examples/02_cardio_small/run_example.sh b/examples/02_cardio_small/run_example.sh
@@ -48,42 +48,42 @@ WF_ID=`fractal --batch workflow new "$WF_NAME" $PRJ_ID`
 echo "WF_ID: $WF_ID"
 
 # Add tasks to workflow
-fractal --batch workflow add-task $WF_ID "Create OME-Zarr structure" --args-file Parameters/create_zarr_structure.json --meta-file Parameters/example_meta.json
-fractal --batch workflow add-task $WF_ID "Convert Yokogawa to OME-Zarr"
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Create OME-Zarr structure" --args-file Parameters/create_zarr_structure.json --meta-file Parameters/example_meta.json
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Convert Yokogawa to OME-Zarr"
 
 echo "{\"overwrite\": \"True\", \"dict_corr\": {\"root_path_corr\": \"`pwd`/../illum_corr_images/\", \"A01_C01\": \"20220621_UZH_manual_illumcorr_40x_A01_C01.png\", \"A01_C02\": \"20220621_UZH_manual_illumcorr_40x_A01_C02.png\", \"A02_C03\": \"20220621_UZH_manual_illumcorr_40x_A02_C03.png\"}}" > Parameters/illumination_correction.json
-fractal --batch workflow add-task $WF_ID "Illumination correction" --args-file Parameters/illumination_correction.json
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Illumination correction" --args-file Parameters/illumination_correction.json
 
 # 3D Segmentation & measurements
-fractal --batch workflow add-task $WF_ID "Cellpose Segmentation" --args-file Parameters/cellpose_segmentation_3D.json --meta-file Parameters/meta_cellpose.json
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Cellpose Segmentation" --args-file Parameters/cellpose_segmentation_3D.json --meta-file Parameters/meta_cellpose.json
 echo "{\"level\": 0, \"input_ROI_table\": \"FOV_ROI_table\", \"workflow_file\": \"${HERE}/regionprops_from_existing_labels_feature.yaml\", \"input_specs\": {\"dapi_img\": {\"type\": \"image\", \"wavelength_id\": \"A01_C01\"}, \"label_img\": {\"type\": \"label\", \"label_name\": \"nuclei\"}}, \"output_specs\": {\"regionprops_DAPI\": {\"type\": \"dataframe\", \"table_name\": \"regionprops_DAPI\"}}}" > Parameters/measurements_3D.json
-fractal --batch workflow add-task $WF_ID "Napari workflows wrapper" --args-file Parameters/measurements_3D.json
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Napari workflows wrapper" --args-file Parameters/measurements_3D.json
 
 
 # Maximum intensity projection
-fractal --batch workflow add-task $WF_ID "Copy OME-Zarr structure"
-fractal --batch workflow add-task $WF_ID "Maximum Intensity Projection"
-fractal --batch workflow add-task $WF_ID "Cellpose Segmentation" --args-file Parameters/cellpose_segmentation.json --meta-file Parameters/meta_cellpose.json
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Copy OME-Zarr structure"
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Maximum Intensity Projection"
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Cellpose Segmentation" --args-file Parameters/cellpose_segmentation.json --meta-file Parameters/meta_cellpose.json
 
 # Run a series of napari workflows
 echo "{\"level\": 0, \"input_ROI_table\": \"well_ROI_table\", \"workflow_file\": \"${HERE}/regionprops_from_existing_labels_feature.yaml\", \"input_specs\": {\"dapi_img\": {\"type\": \"image\", \"wavelength_id\": \"A01_C01\"}, \"label_img\": {\"type\": \"label\", \"label_name\": \"nuclei\"}}, \"output_specs\": {\"regionprops_DAPI\": {\"type\": \"dataframe\", \"table_name\": \"regionprops_DAPI\"}}}" > Parameters/measurement.json
-fractal --batch workflow add-task $WF_ID "Napari workflows wrapper" --args-file Parameters/measurement.json
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Napari workflows wrapper" --args-file Parameters/measurement.json
 
 # # Workflow 2: 
 echo "{\"level\": 0, \"input_ROI_table\": \"well_ROI_table\", \"workflow_file\": \"${HERE}/np_wf_2_label.yaml\", \"input_specs\": {\"slice_img\": {\"type\": \"image\", \"wavelength_id\": \"A01_C01\"}, \"slice_img_c2\": {\"type\": \"image\", \"wavelength_id\": \"A02_C03\"}}, \"output_specs\": {\"Result of Expand labels (scikit-image, nsbatwm)\": {\"type\": \"label\", \"label_name\": \"wf_2_labels\"}}}" > Parameters/measurement2.json
-fractal --batch workflow add-task $WF_ID "Napari workflows wrapper" --args-file Parameters/measurement2.json
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Napari workflows wrapper" --args-file Parameters/measurement2.json
 
 # Workflow 3: 
 echo "{\"level\": 0, \"input_ROI_table\": \"well_ROI_table\", \"workflow_file\": \"${HERE}/np_wf_3_label_df.yaml\", \"input_specs\": {\"slice_img\": {\"type\": \"image\", \"wavelength_id\": \"A01_C01\"}, \"slice_img_c2\": {\"type\": \"image\", \"wavelength_id\": \"A02_C03\"}}, \"output_specs\": {\"Result of Expand labels (scikit-image, nsbatwm)\": {\"type\": \"label\", \"label_name\": \"wf_3_labels\"}, \"regionprops_DAPI\": {\"type\": \"dataframe\", \"table_name\": \"nuclei_measurements_wf3\"}}}" > Parameters/measurement3.json
-fractal --batch workflow add-task $WF_ID "Napari workflows wrapper" --args-file Parameters/measurement3.json
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Napari workflows wrapper" --args-file Parameters/measurement3.json
 
 # Workflow 4: 
 echo "{\"level\": 0, \"input_ROI_table\": \"well_ROI_table\", \"workflow_file\": \"${HERE}/np_wf_4_label_multi_df.yaml\", \"input_specs\": {\"slice_img\": {\"type\": \"image\", \"wavelength_id\": \"A01_C01\"}, \"slice_img_c2\": {\"type\": \"image\", \"wavelength_id\": \"A02_C03\"}}, \"output_specs\": {\"Result of Expand labels (scikit-image, nsbatwm)\": {\"type\": \"label\", \"label_name\": \"wf_4_labels\"}, \"regionprops_DAPI\": {\"type\": \"dataframe\", \"table_name\": \"nuclei_measurements_wf4\"}, \"regionprops_Lamin\": {\"type\": \"dataframe\",\"table_name\": \"nuclei_lamin_measurements_wf4\"}}}" > Parameters/measurement4.json
-fractal --batch workflow add-task $WF_ID "Napari workflows wrapper" --args-file Parameters/measurement4.json
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Napari workflows wrapper" --args-file Parameters/measurement4.json
 
 # Look at the current workflows
 # fractal workflow show $WF_ID
 # echo
 
 # Apply workflow
-fractal workflow apply -o $DS_OUT_ID -p $PRJ_ID $WF_ID $DS_IN_ID
+fractal workflow apply $PRJ_ID $WF_ID $DS_IN_ID $DS_OUT_ID
diff --git a/examples/02_cardio_small/run_example_on_image_subset.sh b/examples/02_cardio_small/run_example_on_image_subset.sh
@@ -23,6 +23,8 @@ HERE=`pwd`
 export FRACTAL_CACHE_PATH=`pwd`/".cache"
 rm -rv ${FRACTAL_CACHE_PATH} 2> /dev/null
 
+###############################################################################
+
 # Create project
 OUTPUT=`fractal --batch project new $PRJ_NAME`
 PRJ_ID=`echo $OUTPUT | cut -d ' ' -f1`
@@ -46,42 +48,42 @@ WF_ID=`fractal --batch workflow new "$WF_NAME" $PRJ_ID`
 echo "WF_ID: $WF_ID"
 
 # Add tasks to workflow
-fractal --batch workflow add-task $WF_ID "Create OME-Zarr structure" --args-file Parameters/create_zarr_structure_image_subset.json --meta-file Parameters/example_meta.json
-fractal --batch workflow add-task $WF_ID "Convert Yokogawa to OME-Zarr"
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Create OME-Zarr structure" --args-file Parameters/create_zarr_structure_image_subset.json --meta-file Parameters/example_meta.json
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Convert Yokogawa to OME-Zarr"
 
 echo "{\"overwrite\": \"True\", \"dict_corr\": {\"root_path_corr\": \"`pwd`/../illum_corr_images/\", \"A01_C01\": \"20220621_UZH_manual_illumcorr_40x_A01_C01.png\", \"A01_C02\": \"20220621_UZH_manual_illumcorr_40x_A01_C02.png\", \"A02_C03\": \"20220621_UZH_manual_illumcorr_40x_A02_C03.png\"}}" > Parameters/illumination_correction.json
-fractal --batch workflow add-task $WF_ID "Illumination correction" --args-file Parameters/illumination_correction.json
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Illumination correction" --args-file Parameters/illumination_correction.json
 
 # 3D Segmentation & measurements
-fractal --batch workflow add-task $WF_ID "Cellpose Segmentation" --args-file Parameters/cellpose_segmentation_3D.json
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Cellpose Segmentation" --args-file Parameters/cellpose_segmentation_3D.json
 echo "{\"level\": 0, \"input_ROI_table\": \"FOV_ROI_table\", \"workflow_file\": \"${HERE}/regionprops_from_existing_labels_feature.yaml\", \"input_specs\": {\"dapi_img\": {\"type\": \"image\", \"wavelength_id\": \"A01_C01\"}, \"label_img\": {\"type\": \"label\", \"label_name\": \"nuclei\"}}, \"output_specs\": {\"regionprops_DAPI\": {\"type\": \"dataframe\", \"table_name\": \"regionprops_DAPI\"}}}" > Parameters/measurements_3D.json
-fractal --batch workflow add-task $WF_ID "Napari workflows wrapper" --args-file Parameters/measurements_3D.json
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Napari workflows wrapper" --args-file Parameters/measurements_3D.json
 
 
 # Maximum intensity projection
-fractal --batch workflow add-task $WF_ID "Copy OME-Zarr structure"
-fractal --batch workflow add-task $WF_ID "Maximum Intensity Projection"
-fractal --batch workflow add-task $WF_ID "Cellpose Segmentation" --args-file Parameters/cellpose_segmentation.json #--meta-file Parameters/example_meta.json
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Copy OME-Zarr structure"
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Maximum Intensity Projection"
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Cellpose Segmentation" --args-file Parameters/cellpose_segmentation.json #--meta-file Parameters/example_meta.json
 
 # Run a series of napari workflows
 echo "{\"level\": 0, \"input_ROI_table\": \"well_ROI_table\", \"workflow_file\": \"${HERE}/regionprops_from_existing_labels_feature.yaml\", \"input_specs\": {\"dapi_img\": {\"type\": \"image\", \"wavelength_id\": \"A01_C01\"}, \"label_img\": {\"type\": \"label\", \"label_name\": \"nuclei\"}}, \"output_specs\": {\"regionprops_DAPI\": {\"type\": \"dataframe\", \"table_name\": \"regionprops_DAPI\"}}}" > Parameters/measurement.json
-fractal --batch workflow add-task $WF_ID "Napari workflows wrapper" --args-file Parameters/measurement.json
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Napari workflows wrapper" --args-file Parameters/measurement.json
 
 # # Workflow 2: 
 echo "{\"level\": 0, \"input_ROI_table\": \"well_ROI_table\", \"workflow_file\": \"${HERE}/np_wf_2_label.yaml\", \"input_specs\": {\"slice_img\": {\"type\": \"image\", \"wavelength_id\": \"A01_C01\"}, \"slice_img_c2\": {\"type\": \"image\", \"wavelength_id\": \"A02_C03\"}}, \"output_specs\": {\"Result of Expand labels (scikit-image, nsbatwm)\": {\"type\": \"label\", \"label_name\": \"wf_2_labels\"}}}" > Parameters/measurement2.json
-fractal --batch workflow add-task $WF_ID "Napari workflows wrapper" --args-file Parameters/measurement2.json
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Napari workflows wrapper" --args-file Parameters/measurement2.json
 
 # Workflow 3: 
 echo "{\"level\": 0, \"input_ROI_table\": \"well_ROI_table\", \"workflow_file\": \"${HERE}/np_wf_3_label_df.yaml\", \"input_specs\": {\"slice_img\": {\"type\": \"image\", \"wavelength_id\": \"A01_C01\"}, \"slice_img_c2\": {\"type\": \"image\", \"wavelength_id\": \"A02_C03\"}}, \"output_specs\": {\"Result of Expand labels (scikit-image, nsbatwm)\": {\"type\": \"label\", \"label_name\": \"wf_3_labels\"}, \"regionprops_DAPI\": {\"type\": \"dataframe\", \"table_name\": \"nuclei_measurements_wf3\"}}}" > Parameters/measurement3.json
-fractal --batch workflow add-task $WF_ID "Napari workflows wrapper" --args-file Parameters/measurement3.json
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Napari workflows wrapper" --args-file Parameters/measurement3.json
 
 # Workflow 4: 
 echo "{\"level\": 0, \"input_ROI_table\": \"well_ROI_table\", \"workflow_file\": \"${HERE}/np_wf_4_label_multi_df.yaml\", \"input_specs\": {\"slice_img\": {\"type\": \"image\", \"wavelength_id\": \"A01_C01\"}, \"slice_img_c2\": {\"type\": \"image\", \"wavelength_id\": \"A02_C03\"}}, \"output_specs\": {\"Result of Expand labels (scikit-image, nsbatwm)\": {\"type\": \"label\", \"label_name\": \"wf_4_labels\"}, \"regionprops_DAPI\": {\"type\": \"dataframe\", \"table_name\": \"nuclei_measurements_wf4\"}, \"regionprops_Lamin\": {\"type\": \"dataframe\",\"table_name\": \"nuclei_lamin_measurements_wf4\"}}}" > Parameters/measurement4.json
-fractal --batch workflow add-task $WF_ID "Napari workflows wrapper" --args-file Parameters/measurement4.json
+fractal --batch workflow add-task $PRJ_ID $WF_ID "Napari workflows wrapper" --args-file Parameters/measurement4.json
 
 # Look at the current workflows
 # fractal workflow show $WF_ID
 # echo
 
 # Apply workflow
-fractal workflow apply -o $DS_OUT_ID -p $PRJ_ID $WF_ID $DS_IN_ID
+fractal workflow apply $PRJ_ID $WF_ID $DS_IN_ID $DS_OUT_ID
diff --git a/examples/09_md_conversion_test/.gitignore b/examples/09_md_conversion_test/.gitignore
@@ -0,0 +1,5 @@
+tmp*
+output*
+task_list
+.fractal.env
+proj*
diff --git a/examples/09_md_conversion_test/Parameters/.gitignore b/examples/09_md_conversion_test/Parameters/.gitignore
@@ -0,0 +1 @@
+args_measurement.json
diff --git a/examples/09_md_conversion_test/Parameters/args_cellpose_segmentation.json b/examples/09_md_conversion_test/Parameters/args_cellpose_segmentation.json
@@ -0,0 +1,8 @@
+{
+    "level": 2, 
+    "channel_label": "Maximum-Projection_DAPI",
+    "output_label_name": "organoids", 
+    "input_ROI_table": "well_ROI_table",
+    "model_type": "nuclei",
+    "diameter_level0": 600
+}
diff --git a/examples/09_md_conversion_test/Parameters/args_create_ome_zarr.json b/examples/09_md_conversion_test/Parameters/args_create_ome_zarr.json
@@ -0,0 +1,3 @@
+{
+    "mode": "top-level"
+}
diff --git a/examples/09_md_conversion_test/Parameters/example_meta.json b/examples/09_md_conversion_test/Parameters/example_meta.json
@@ -0,0 +1,4 @@
+{
+    "cpus_per_task": 1,
+    "mem": 4000
+}
diff --git a/examples/09_md_conversion_test/README.md b/examples/09_md_conversion_test/README.md
@@ -0,0 +1,19 @@
+# Setting up a fractal client & run a workflow through Fractal
+Run a Fractal workflow with Molecular Devices Image Xpress data as input.
+
+## Client setup (from `00_user_setup` folder)
+This only needs to be done once (unless the server is restarted again). Follow the instructions in the `00_user_setup` folder.
+
+## Running an example through Fractal
+This needs to be done in each example folder you're running
+1. Switch to this example folder. If you followed the instructions above, credentials should be used automatically. Alternatively, check the top of the script to set them up manually.
+2. Get the example data: Currently just available at FMI.
+3. Make sure the MD tasks are installed. Follow instructions here: https://github.com/jluethi/fractal-faim-hcs 
+4. One can then either go through the project creation, dataset creation, workflow creation & submission one by one. Or run it all at once by running: `. ./run_example.sh`
+
+This should complete fairly quickly (submitting the script to it being finished took 30s on my machine). One can check the status with `fractal job show ID` (where the ID is the job ID of the submitted workflow, 1 for the first workflow submitted. This is shown when submitting the workflow)
+
+Check the client documentation for details on using the Fractal Client: https://fractal-analytics-platform.github.io/fractal/install.html
+Check the Fractal Tasks Core documentation for details on the individual tasks of this example workflow: https://fractal-analytics-platform.github.io/fractal-tasks-core/
+
+Successfully run with `fractal-server==1.3.0a5`, `fractal-client==1.3.0a3` and `fractal-tasks-core==0.10.0a3`
diff --git a/examples/09_md_conversion_test/regionprops_from_existing_labels_feature.yaml b/examples/09_md_conversion_test/regionprops_from_existing_labels_feature.yaml
@@ -0,0 +1,12 @@
+!!python/object:napari_workflows._workflow.Workflow
+_tasks:
+  regionprops_DAPI: !!python/tuple
+  - !!python/name:napari_skimage_regionprops._regionprops.regionprops_table ''
+  - dapi_img
+  - label_img
+  - true
+  - true
+  - false
+  - false
+  - false
+  - false