Add scmultiplex example 08 for organoid data

jluethi · jluethi · commit c2843997816e · 2023-04-19T18:21:39.000+02:00
diff --git a/examples/08_scMultipleX_task/Parameters/.gitignore b/examples/08_scMultipleX_task/Parameters/.gitignore
@@ -0,0 +1 @@
+measurement.json
diff --git a/examples/08_scMultipleX_task/Parameters/cellpose_segmentation_overlap.json b/examples/08_scMultipleX_task/Parameters/cellpose_segmentation_overlap.json
@@ -0,0 +1,11 @@
+{
+    "wavelength_id": "A01_C01",
+    "level": 2,
+    "input_ROI_table": "well_ROI_table",
+    "diameter_level0": 400,
+    "cellprob_threshold": -3.0,
+    "flow_threshold": 0.4,
+    "model_type": "cyto2",
+    "output_label_name": "organoids",
+    "output_ROI_table": "organoid_ROI_table"
+}
diff --git a/examples/08_scMultipleX_task/Parameters/create_zarr_structure.json b/examples/08_scMultipleX_task/Parameters/create_zarr_structure.json
@@ -0,0 +1,34 @@
+{
+    "allowed_channels": [
+        {
+            "wavelength_id": "A01_C01",
+            "colormap": "00FFFF",
+            "end": 2000,
+            "label": "Channel 1",
+            "start": 110
+        },
+        {
+            "wavelength_id": "A02_C02",
+            "colormap": "FF00FF",
+            "end": 500,
+            "label": "Channel 2",
+            "start": 110
+        },
+        {
+            "wavelength_id": "A03_C03",
+            "colormap": "00FF00",
+            "end": 1600,
+            "label": "Channel 3",
+            "start": 110
+        },
+        {
+            "wavelength_id": "A04_C04",
+            "colormap": "FFFF00",
+            "end": 1600,
+            "label": "Channel 4",
+            "start": 110
+        }
+    ],
+    "coarsening_xy": 2,
+    "num_levels": 5
+}
diff --git a/examples/08_scMultipleX_task/Parameters/create_zarr_structure_subset.json b/examples/08_scMultipleX_task/Parameters/create_zarr_structure_subset.json
@@ -0,0 +1,35 @@
+{
+    "allowed_channels": [
+        {
+            "wavelength_id": "A01_C01",
+            "colormap": "00FFFF",
+            "end": 2000,
+            "label": "Channel 1",
+            "start": 110
+        },
+        {
+            "wavelength_id": "A02_C02",
+            "colormap": "FF00FF",
+            "end": 500,
+            "label": "Channel 2",
+            "start": 110
+        },
+        {
+            "wavelength_id": "A03_C03",
+            "colormap": "00FF00",
+            "end": 1600,
+            "label": "Channel 3",
+            "start": 110
+        },
+        {
+            "wavelength_id": "A04_C04",
+            "colormap": "FFFF00",
+            "end": 1600,
+            "label": "Channel 4",
+            "start": 110
+        }
+    ],
+    "coarsening_xy": 2,
+    "num_levels": 5,
+    "image_glob_patterns": ["*F007L*"]
+}
diff --git a/examples/08_scMultipleX_task/Parameters/scmultiplex.json b/examples/08_scMultipleX_task/Parameters/scmultiplex.json
@@ -0,0 +1,14 @@
+{
+    "level": 0,
+    "label_level": 0,
+    "input_ROI_table": "well_ROI_table",
+    "input_channels": {
+        "C01": {"wavelength_id": "A01_C01"},
+        "C02": {"wavelength_id": "A02_C02"},
+        "C03": {"wavelength_id": "A03_C03"},
+        "C04": {"wavelength_id": "A04_C04"}
+    },
+    "label_image": "organoids",
+    "output_table_name": "organoids",
+    "measure_morphology": true
+}
diff --git a/examples/08_scMultipleX_task/Parameters_tiny/.gitignore b/examples/08_scMultipleX_task/Parameters_tiny/.gitignore
@@ -0,0 +1 @@
+args_measurement.json
diff --git a/examples/08_scMultipleX_task/Parameters_tiny/args_cellpose_segmentation.json b/examples/08_scMultipleX_task/Parameters_tiny/args_cellpose_segmentation.json
@@ -0,0 +1,8 @@
+{
+    "level": 2, 
+    "wavelength_id": "A01_C01", 
+    "output_label_name": "nuclei", 
+    "input_ROI_table": "well_ROI_table",
+    "model_type": "nuclei",
+    "diameter_level0": 60
+}
diff --git a/examples/08_scMultipleX_task/Parameters_tiny/args_create_ome_zarr.json b/examples/08_scMultipleX_task/Parameters_tiny/args_create_ome_zarr.json
@@ -0,0 +1,29 @@
+{
+    "allowed_channels": [
+        {
+            "colormap": "00FFFF",
+            "wavelength_id": "A01_C01",
+            "end": 800,
+            "label": "DAPI",
+            "start": 110
+        },
+        {
+            "colormap": "FF00FF",
+            "end": 290,
+            "wavelength_id": "A01_C02",
+            "label": "nanog",
+            "start": 110
+        },
+        {
+            "colormap": "FFFF00",
+            "end": 1600,
+            "wavelength_id": "A02_C03",
+            "label": "Lamin B1",
+            "start": 110
+        }
+        ]
+    ,
+    "coarsening_xy": 2,
+    "num_levels": 5,
+    "image_extension": "png"
+}
diff --git a/examples/08_scMultipleX_task/Parameters_tiny/example_meta.json b/examples/08_scMultipleX_task/Parameters_tiny/example_meta.json
@@ -0,0 +1 @@
+{"executor": "cpu-mid"}
diff --git a/examples/08_scMultipleX_task/Parameters_tiny/scmultiplex.json b/examples/08_scMultipleX_task/Parameters_tiny/scmultiplex.json
@@ -0,0 +1,11 @@
+{
+    "level": 0,
+    "label_level": 0,
+    "input_ROI_table": "well_ROI_table",
+    "input_channels": {
+        "C01": {"wavelength_id": "A01_C01"}
+    },
+    "label_image": "nuclei",
+    "output_table_name": "nuclei",
+    "measure_morphology": true
+}
diff --git a/examples/08_scMultipleX_task/run_scmultiplex_workflow.sh b/examples/08_scMultipleX_task/run_scmultiplex_workflow.sh
@@ -0,0 +1,83 @@
+LABEL="scmultiplex-7"
+
+# Get the credentials: If you followed the instructions, they can be copied 
+# from the .fractal.env file in ../00_user_setup. Alternatively, you can write
+# a .fractal.env file yourself or add --user & --password entries to all fractal
+# commands below
+cp ../00_user_setup/.fractal.env .fractal.env
+
+# Initialization for some environment variables for the worker
+# Needed on clusters where users don't have write access to the conda env and 
+# fractal user cache directories
+BASE_CACHE_DIR=${HOME}/.cache
+WORKER_INIT="\
+export CELLPOSE_LOCAL_MODELS_PATH=$BASE_CACHE_DIR/CELLPOSE_LOCAL_MODELS_PATH
+export NUMBA_CACHE_DIR=$BASE_CACHE_DIR/NUMBA_CACHE_DIR
+export NAPARI_CONFIG=$BASE_CACHE_DIR/napari_config.json
+export XDG_CONFIG_HOME=$BASE_CACHE_DIR/XDG_CONFIG
+export XDG_CACHE_HOME=$BASE_CACHE_DIR/XDG
+"
+
+# Set useful variables
+PRJ_NAME="proj-$LABEL"
+DS_IN_NAME="input-ds-$LABEL"
+DS_OUT_NAME="output-ds-$LABEL"
+WF_NAME="Workflow $LABEL"
+
+# Set cache path and remove any previous file from there
+export FRACTAL_CACHE_PATH=`pwd`/".cache"
+rm -rv ${FRACTAL_CACHE_PATH} 2> /dev/null
+
+# Define/initialize empty project folder and temporary file
+PROJ_DIR=`pwd`/tmp_${LABEL}
+rm -r $PROJ_DIR 2> /dev/null
+mkdir $PROJ_DIR
+
+###############################################################################
+# IMPORTANT: modify the following lines so that they point to absolute paths
+# INPUT_PATH=/data/active/fractal/Liberali/1_well_15_fields_20_planes_SF_w_errors/D10_R1/220304_172545_220304_175557
+# OUTPUT_PATH=/data/active/jluethi/Fractal/20230316_$LABEL
+INPUT_PATH=/Users/joel/shares/dataShareFractal/fractal/Liberali/1_well_15_fields_20_planes_SF_w_errors/D10_R1/220304_172545_220304_175557
+OUTPUT_PATH=/Users/joel/Desktop/Zarr_$LABEL
+###############################################################################
+
+# Create project
+OUTPUT=`fractal --batch project new $PRJ_NAME $PROJ_DIR`
+PRJ_ID=`echo $OUTPUT | cut -d ' ' -f1`
+DS_IN_ID=`echo $OUTPUT | cut -d ' ' -f2`
+echo "PRJ_ID: $PRJ_ID"
+echo "DS_IN_ID: $DS_IN_ID"
+
+# Update dataset name/type, and add a resource
+fractal dataset edit --new-name "$DS_IN_NAME" --new-type image --make-read-only $PRJ_ID $DS_IN_ID
+fractal dataset add-resource $PRJ_ID $DS_IN_ID $INPUT_PATH
+
+# Add output dataset, and add a resource to it
+DS_OUT_ID=`fractal --batch project add-dataset $PRJ_ID "$DS_OUT_NAME"`
+echo "DS_OUT_ID: $DS_OUT_ID"
+
+fractal dataset edit --new-type zarr --remove-read-only $PRJ_ID $DS_OUT_ID
+fractal dataset add-resource $PRJ_ID $DS_OUT_ID $OUTPUT_PATH
+
+# Create workflow
+WF_ID=`fractal --batch workflow new "$WF_NAME" $PRJ_ID`
+echo "WF_ID: $WF_ID"
+
+# Add tasks to workflow
+fractal workflow add-task $WF_ID "Create OME-Zarr structure" --args-file Parameters/create_zarr_structure.json
+fractal workflow add-task $WF_ID "Convert Yokogawa to OME-Zarr"
+
+fractal workflow add-task $WF_ID "Copy OME-Zarr structure"
+fractal workflow add-task $WF_ID "Maximum Intensity Projection"
+
+# Organoid segmentation
+fractal workflow add-task $WF_ID "Cellpose Segmentation" --args-file Parameters/cellpose_segmentation_overlap.json
+
+fractal workflow add-task $WF_ID "ScMultipleX Measurement" --args-file Parameters/scmultiplex.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 $DS_IN_ID --worker-init "$WORKER_INIT"
