add support for writing omero metadata (#6)

khanlab · Feb 22, 2024 · 342ecdb · 342ecdb
1 parent 6c80276
commit 342ecdb
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Showing 3 changed files with 43 additions and 2 deletions.
diff --git a/config/config.yml b/config/config.yml
@@ -43,6 +43,31 @@ ome_zarr:
     - 1024
     - 1024
   scaling_method: 'local_mean' #can be nearest, gaussian, local_mean, zoom (zoom uses spline interp)
+
+  omero_metadata:
+    channels:
+      default_color: 'FFFFFF'
+      color_mapping:
+        autof: 'FFFFFF'
+        abeta: '00FF00'
+      defaults:
+        active: True
+        coefficient: 1.0
+        inverted: False
+        family: linear
+        window: 
+          min: 0
+          max: 65535
+          start: 0
+          end: 65535
+    defaults:
+      rdefs:
+        defaultT: 0
+        defaultZ: 0
+        model: 'color'
+      id: 0
+      name: spim
+      version: "0.4"  
 
 nifti:
   levels: #cannot be higher than max_downsampling_layers in ome_zarr

diff --git a/workflow/rules/ome_zarr.smk b/workflow/rules/ome_zarr.smk
@@ -21,6 +21,7 @@ rule zarr_to_ome_zarr:
         rechunk_size=config["ome_zarr"]["rechunk_size"],
         scaling_method=config["ome_zarr"]["scaling_method"],
         downsampling=config["bigstitcher"]["fuse_dataset"]["downsampling"],
+        stains=get_stains,
     output:
         zarr=temp(
             directory(

diff --git a/workflow/scripts/zarr_to_ome_zarr.py b/workflow/scripts/zarr_to_ome_zarr.py
@@ -13,6 +13,7 @@
 max_layer=snakemake.params.max_downsampling_layers #number of downsamplings by 2 to include in zarr
 rechunk_size=snakemake.params.rechunk_size
 out_zarr=snakemake.output.zarr
+stains=snakemake.params.stains
 scaling_method=snakemake.params.scaling_method
 
 # prepare metadata for ome-zarr
@@ -37,16 +38,28 @@
 axes =  [{'name': 'c', 'type': 'channel'}] + [{'name': ax, 'type': 'space', 'unit': 'micrometer'} for ax in ['z','y','x'] ] 
 
 
+#init omero metadata
+omero={key:val for key,val in snakemake.config['ome_zarr']['omero_metadata']['defaults'].items()}
+omero['channels']=[]
+
 darr_list=[]
 for zarr_i in range(len(snakemake.input.zarr)):
-
     #open zarr to get group name
     in_zarr=snakemake.input.zarr[zarr_i]
     zi = zarr.open(in_zarr)
     group_name = [g for g in zi.group_keys()][0]
 
     darr_list.append(da.from_zarr(in_zarr,component=f'{group_name}/s0',chunks=rechunk_size))
 
+    #append to omero metadata
+    channel_metadata={key:val for key,val in snakemake.config['ome_zarr']['omero_metadata']['channels']['defaults'].items()}
+    channel_name=stains[zarr_i]
+    channel_metadata['label'] = channel_name
+    default_color=snakemake.config['ome_zarr']['omero_metadata']['channels']['default_color']
+    color=snakemake.config['ome_zarr']['omero_metadata']['channels']['color_mapping'].get(channel_name,default_color)
+    channel_metadata['color'] = color
+    omero['channels'].append(channel_metadata)
+
 
 darr_channels = da.stack(darr_list)
 
@@ -63,6 +76,8 @@
                             scaler=scaler,
                             coordinate_transformations=coordinate_transformations,
                             storage_options={'dimension_separator': '/'},
-                            axes=axes)
+                            axes=axes,
+                            metadata={'omero':omero}
+                                )