JSON for block extraction, small fixes

Author: schilling40

flamingo_tools/segmentation/sgn_detection.py

@@ -149,7 +149,7 @@ def sgn_detection(
     detection_path = os.path.join(output_folder, "SGN_detection.tsv")
     input_ = zarr.open(output_path, "r")[prediction_key]
     if not os.path.exists(detection_path):
-        block_shape = (128, 128, 128)  # bigger block to avoid edge effects
+        block_shape = (12, 128, 128)  # bigger block to avoid edge effects
         detections_maxima = find_local_maxima(
             input_, block_shape=block_shape, min_distance=min_distance, threshold_abs=threshold_abs,
             verbose=True, n_threads=16,

flamingo_tools/segmentation/unet_prediction.py

@@ -230,6 +230,10 @@ def find_mask(
         upper_percentile = 99
         min_intensity = 150
         print(f"Calculating mask for segmentation class {seg_class}.")
+    elif seg_class == "ihc_low":
+        upper_percentile = 99.5
+        min_intensity = 100
+        print(f"Calculating mask for segmentation class {seg_class}.")
     else:
         upper_percentile = 95
         min_intensity = 200

reproducibility/block_extraction/LaVision_IHC_Mar05.json

@@ -0,0 +1,37 @@
+[
+	{
+		"cochlea": "LaVision-Mar05",
+		"image_channel": [
+			"MYO",
+			"PV",
+			"IHC_LOWRES-v3"
+		],
+		"resolution" : [
+			1.887779, 
+			1.887779,
+			3.0 
+		],
+		"halo_size": [
+			128,
+			128,
+			32
+		],
+		"crop_centers": [
+			[
+				3077,
+				3000,
+				960
+			],
+			[
+				2816,
+				3170,
+				320
+			],
+			[
+				2410,
+				3080,
+				250
+			]
+		]
+	}
+]

reproducibility/block_extraction/SGNsub_MLR184L.json

@@ -19,34 +19,34 @@
 		],
 		"crop_centers": [
 			[
-				864,
-				1058,
+				887,
+				1057,
 				580
 			],
 			[
-				911,
-				764,
-				605
+				887,
+				735,
+				592
 			],
 			[
-				586,
-				724,
-				542
+				538,
+				766,
+				558
 			],
 			[
-				519,
-				900,
-				786
+				525,
+				869,
+				873
 			],
 			[
-				648,
-				696,
-				999
+				695,
+				582,
+				1010
 			],
 			[
-				716,
-				357,
-				975
+				615,
+				231,
+				950
 			]
 		]
 	}

reproducibility/block_extraction/SGNsub_MLR99L.json

@@ -1,6 +1,6 @@
 [
 	{
-		"cochlea": "M_LR_000214_L",
+		"cochlea": "M_LR_000099_L",
 		"image_channel": [
 			"PV",
 			"Calb1",
@@ -20,34 +20,34 @@
 		],
 		"crop_centers": [
 			[
-				617,
-				914,
-				690
+				979,
+				1250,
+				1060
 			],
 			[
-				614,
-				709,
-				477
+				1230,
+				1066,
+				1037
 			],
 			[
-				311,
-				747,
-				472
+				1057,
+				819,
+				1039
 			],
 			[
-				283,
-				634,
-				772
+				951,
+				839,
+				722
 			],
 			[
-				424,
-				332,
-				780
+				1260,
+				859,
+				551
 			],
 			[
-				383,
-				69,
-				571
+				1542,
+				647,
+				540
 			]
 		]
 	}

reproducibility/tonotopic_mapping/MLR184L.json

@@ -0,0 +1,10 @@
+[
+    {
+		"cochlea": "M_LR_000184_L",
+		"component_list": [
+			1
+		],
+		"segmentation_channel": "SGN_v2",
+		"type": "sgn"
+	}
+]									

reproducibility/tonotopic_mapping/MLR184R.json

@@ -0,0 +1,10 @@
+[
+    {
+		"cochlea": "M_LR_000184_R",
+		"component_list": [
+			1
+		],
+		"segmentation_channel": "SGN_v2",
+		"type": "sgn"
+	}
+]									

scripts/export_lower_resolution.py

@@ -165,6 +165,9 @@ def export_lower_resolution(args):
                 if "PV" in channel:
                     max_intensity = 1400
                     data[data > max_intensity] = 0
+                if "CTBP2" in channel:
+                    max_intensity = 1400
+                    data[data > max_intensity] = 300
 
             if args.binarize:
                 data = (data > 0).astype("uint16")