Tonotopic mapping for OTOF cochleae

Author: schilling40

flamingo_tools/segmentation/cochlea_mapping.py

@@ -519,7 +519,7 @@ def measure_run_length_ihcs(
     return total_distance, path, path_dict
 
 
-def map_frequency(table: pd.DataFrame, animal: str = "mouse") -> pd.DataFrame:
+def map_frequency(table: pd.DataFrame, animal: str = "mouse", otof: bool = False) -> pd.DataFrame:
     """Map the frequency range of SGNs in the cochlea
     using Greenwood function f(x) = A * (10 **(ax) - K).
     Values for humans: a=2.1, k=0.88, A = 165.4 [kHz].
@@ -543,6 +543,7 @@ def map_frequency(table: pd.DataFrame, animal: str = "mouse") -> pd.DataFrame:
     elif animal == "gerbil":
         # freq_min = 0.0105 kHz
         # freq_max = 43.82 kHz
+        # values used by keppeler, PNAS 2021 Vol. 118 No. 18, https://doi.org/10.1073/pnas.2014472118
         var_A = 0.35
         var_a = 2.1
         var_k = 0.7
@@ -553,6 +554,17 @@ def map_frequency(table: pd.DataFrame, animal: str = "mouse") -> pd.DataFrame:
     table.loc[table['offset'] >= 0, 'frequency[kHz]'] = var_A * (10 ** (var_a * table["length_fraction"]) - var_k)
     table.loc[table['offset'] < 0, 'frequency[kHz]'] = 0
 
+    if otof and animal == "mouse":
+        # freq_min = 4.84 kHz
+        # freq_max = 78.8 kHz
+        # Mueller, Hearing Research 202 (2005) 63–73, https://doi.org/10.1016/j.heares.2004.08.011
+        # function has format f(x) = 10 ** (a * (k - (1-x)))
+        var_a = 100 / 82.5
+        var_k = 1.565
+        var_A = 1
+        table.loc[table['offset'] >= 0, 'frequency-mueller[kHz]'] = var_A * (10 ** (var_a * (var_k - (1 - table["length_fraction"])))) # noqa
+        table.loc[table['offset'] < 0, 'frequency-mueller[kHz]'] = 0
+
     return table
 
 
@@ -727,6 +739,7 @@ def tonotopic_mapping(
     animal: str = "mouse",
     max_edge_distance: float = 30,
     apex_higher: bool = True,
+    otof: bool = False,
 ) -> pd.DataFrame:
     """Tonotopic mapping of IHCs by supplying a table with component labels.
     The mapping assigns a tonotopic label to each IHC according to the position along the length of the cochlea.
@@ -787,6 +800,6 @@ def tonotopic_mapping(
 
     table.loc[:, "length[µm]"] = table["length_fraction"] * total_distance
 
-    table = map_frequency(table, animal=animal)
+    table = map_frequency(table, animal=animal, otof=otof)
 
     return table

reproducibility/block_extraction/LaVision_OTOF23R.json

@@ -0,0 +1,46 @@
+[
+	{
+		"cochlea": "LaVision-OTOF23R",
+		"image_channel": [
+			"CR",
+			"rbOtof",
+			"IHC_LOWRES-v3"
+		],
+		"segmentation_channel": "IHC_LOWRES-v3",
+		"type": "ihc",
+		"resolution": [
+			1.887779,
+			1.887779,
+			3.0
+		],
+		"n_blocks": 3,
+		"max_edge_distance": 200,
+		"component_list": [
+			4,
+			18,
+			7
+		],
+		"halo_size": [
+			256,
+			256,
+			48
+		],
+		"crop_centers": [
+			[
+				1289,
+				1859,
+				247
+			],
+			[
+				2308,
+				3310,
+				642
+			],
+			[
+				1751,
+				1140,
+				710
+			]
+		]
+	}
+]

reproducibility/block_extraction/LaVision_OTOF25R.json

@@ -0,0 +1,54 @@
+[
+	{
+		"cochlea": "LaVision-OTOF25R",
+		"image_channel": [
+			"CR",
+			"rbOtof",
+			"IHC_LOWRES-v3"
+		],
+		"segmentation_channel": "IHC_LOWRES-v3",
+		"type": "ihc",
+		"resolution": [
+			1.887779,
+			1.887779,
+			3.0
+		],
+		"n_blocks": 3,
+		"max_edge_distance": 200,
+		"component_list": [
+			1
+		],
+		"halo_size": [
+			256,
+			256,
+			48
+		],
+		"crop_centers": [
+			[
+				2803,
+				2238,
+				1265
+			],
+			[
+				2781,
+				3351,
+				895
+			],
+			[
+				1105,
+				3380,
+				1020
+			],
+			[
+				1023,
+				2197,
+				1103
+			],
+			[
+				1858,
+				1507,
+				993
+			]
+		]
+	}
+]

reproducibility/object_measures/LaVision-OTOF25R.json

@@ -0,0 +1,18 @@
+[
+	{
+		"cochlea": "LaVision-OTOF25R",
+		"image_channel": [
+			"CR",
+			"rbOtof"
+		],
+		"segmentation_channel": "IHC_LOWRES-v3",
+		"component_list": [
+			1
+		],
+        "resolution" : [
+            1.887779,
+            1.887779,
+            3.0
+        ]
+	}
+]

reproducibility/tonotopic_mapping/repro_tonotopic_mapping.py

@@ -35,6 +35,11 @@ def repro_tonotopic_mapping(
     for dic in param_dicts:
         cochlea = dic["cochlea"]
         seg_channel = dic["segmentation_channel"]
+        if "OTOF" in cochlea:
+            otof = True
+        else:
+            otof = False
+
         if cochlea[0] in ["M", "m"]:
             animal = "mouse"
         elif cochlea[0] in ["G", "g"]:
@@ -71,7 +76,8 @@ def repro_tonotopic_mapping(
         if not os.path.isfile(output_table_path) or force_overwrite:
             table = tonotopic_mapping(table, component_label=component_list, animal=animal,
                                       cell_type=cell_type, component_mapping=component_mapping,
-                                      apex_higher=apex_higher, max_edge_distance=max_edge_distance)
+                                      apex_higher=apex_higher, max_edge_distance=max_edge_distance,
+                                      otof=otof)
 
             table.to_csv(output_table_path, sep="\t", index=False)