update toy dataset config

loic-lb · Jan 9, 2024 · 89ec381 · 89ec381
1 parent c091741
commit 89ec381
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Showing 2 changed files with 6 additions and 7 deletions.
diff --git a/workflow/config/toy/uniform_baysor.yaml b/workflow/config/toy/uniform_baysor.yaml
@@ -3,7 +3,7 @@ read:
   technology: uniform
 
 patchify:
-  patch_width_pixel: 1100
+  patch_width_pixel: 1200
   patch_overlap_pixel: 50
   patch_width_microns: 3000
   patch_overlap_microns: 40
@@ -23,7 +23,7 @@ segmentation:
         confidence_nn_id: 6
 
       segmentation:
-        scale: 20 # typical cell radius
+        scale: 30 # typical cell radius
         scale_std: "25%" # cell radius standard deviation
         prior_segmentation_confidence: 0
         estimate_scale_from_centers: false

diff --git a/workflow/config/toy/uniform_cellpose.yaml b/workflow/config/toy/uniform_cellpose.yaml
@@ -3,19 +3,18 @@ read:
   technology: uniform
 
 patchify:
-  patch_width_pixel: 1100
+  patch_width_pixel: 1200
   patch_overlap_pixel: 50
   patch_width_microns: 3000
   patch_overlap_microns: 40
 
 segmentation:
   cellpose:
-    diameter: 40
+    diameter: 35
     channels: ["DAPI"]
     flow_threshold: 2
     cellprob_threshold: -6
-    min_area: 1000
-    clip_limit: 0.01
+    min_area: 2500
 
 aggregate:
   average_intensities: true
@@ -28,7 +27,7 @@ annotation:
       CK: Tumoral cell
       CD3: T cell
       CD20: B cell
-      
+
 explorer:
   gene_column: "genes"
   ram_threshold_gb: 16