Merge pull request #388 from AllenCellModeling/amil-multchannel-support

🚀 Added plugin support for multi-channel segmentations
AllenCellModeling · Jun 27, 2024 · 6195a66 · 6195a66
2 parents 27f1075 + ba76e97
commit 6195a66
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Showing 2 changed files with 14 additions and 6 deletions.
diff --git a/configs/data/im2im/segmentation_plugin.yaml b/configs/data/im2im/segmentation_plugin.yaml
@@ -33,14 +33,16 @@ transforms:
         reader:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: ${eval:'"CZYX" if ${spatial_dims}==3 else "CYX"'}
-            C: 0
+            # [TRAIN] Exposing C as a configurable param for multi-channel segs
+            C: ${target_col1_channel}
       - _target_: monai.transforms.LoadImaged
         keys: ${target_col2}
         allow_missing_keys: True
         reader:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: ${eval:'"CZYX" if ${spatial_dims}==3 else "CYX"'}
-            C: 0
+            # [TRAIN] Exposing C as a configurable param for multi-channel segs
+            C: ${target_col2_channel}
       - _target_: monai.transforms.ThresholdIntensityd
         allow_missing_keys: True
         keys:
@@ -108,14 +110,16 @@ transforms:
         reader:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: ${eval:'"CZYX" if ${spatial_dims}==3 else "CYX"'}
-            C: 0
+            # [TEST] Exposing C as a configurable param for multi-channel segs
+            C: ${target_col1_channel}
       - _target_: monai.transforms.LoadImaged
         keys: ${target_col2}
         allow_missing_keys: True
         reader:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: ${eval:'"CZYX" if ${spatial_dims}==3 else "CYX"'}
-            C: 0
+            # [TEST] Exposing C as a configurable param for multi-channel segs
+            C: ${target_col2_channel}
       # load merging mask - assumed not to exist by default
       - _target_: cyto_dl.image.io.PolygonLoaderd
         keys:
@@ -184,14 +188,16 @@ transforms:
         reader:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: ${eval:'"CZYX" if ${spatial_dims}==3 else "CYX"'}
-            C: 0
+            # [VAL] Exposing C as a configurable param for multi-channel segs
+            C: ${target_col1_channel}
       - _target_: monai.transforms.LoadImaged
         keys: ${target_col2}
         allow_missing_keys: True
         reader:
           - _target_: cyto_dl.image.io.MonaiBioReader
             dimension_order_out: ${eval:'"CZYX" if ${spatial_dims}==3 else "CYX"'}
-            C: 0
+            # [VAL] Exposing C as a configurable param for multi-channel segs
+            C: ${target_col2_channel}
 
       - _target_: monai.transforms.ThresholdIntensityd
         allow_missing_keys: True

diff --git a/configs/experiment/im2im/segmentation_plugin.yaml b/configs/experiment/im2im/segmentation_plugin.yaml
@@ -29,6 +29,8 @@ test: False
 source_col: raw
 target_col1: seg1
 target_col2: seg2
+target_col1_channel: 0
+target_col2_channel: 0
 merge_mask_col: merge_mask
 exclude_mask_col: exclude_mask
 base_image_col: base_image