Update microscopy-override.yaml

microscopy-override.yaml

@@ -44,15 +44,15 @@ scheduler:
 dataset:
   train_dataset:
     dir:
-        path: [
-        "path/to/train/directory/1",
-        "path/to/train/directory/2",
-        "path/to/train/directory/3",
+      labels_suffix: .tif
+      path: [ # inside each dir_n should be a subdir and subdir_GT/TRA containing the raw images and labelled masks
+      /train/dir_1,
+      /train/dir_2,
+      ...
       ]
-        labels_suffix: ".slp"
-        vid_suffix: ".mp4"
-    clip_length: 32
-    crop_size: [22, 32, 42, 100]
+      vid_suffix: .tif
+    clip_length: 16
+    crop_size: [22, 32,..] # can specify different crop sizes for each of the training directories
     padding: 0
     anchors: "centroid"
     augmentations:
@@ -82,14 +82,15 @@ dataset:
     
   val_dataset:
       dir: 
-        path: [
-        "path/to/val/directory/1",
-        "path/to/val/directory/2",
-      ]
-        labels_suffix: ".slp"
-        vid_suffix: ".mp4"
-      crop_size: [22, 32]
-      clip_length: 32
+        labels_suffix: .tif
+        path: [ # inside each dir_n should be a subdir and subdir_GT/TRA containing the raw images and labelled masks
+        /val/dir_1,
+        /val/dir_2,
+        ...
+        ]
+        vid_suffix: .tif
+      crop_size: [30, 50] # can specify different crop sizes for each of the training directories
+      clip_length: 16
       padding: 0
       anchors: "centroid"
       # subsamples the dataset! e.g. if the dataset would have 1000 chunks of length 32, this would limit the validation set to 300 chunks