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schilling40schilling40
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SGN subtype update: 98L, N152L
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6 files changed

+170
-3
lines changed

6 files changed

+170
-3
lines changed

‎reproducibility/block_extraction/SGNsub_MLR98L.json‎

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[
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{
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"cochlea": "M_LR_000098_L",
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"image_channel": [
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"CR",
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"Ntng1",
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"PV",
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"SGN_v2"
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],
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"segmentation_channel": "SGN_v2",
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"type": "sgn",
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"n_blocks": 6,
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"halo_size": [
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256,
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256,
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50
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],
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"component_list": [
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1,
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2
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],
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"crop_centers": [
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[
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901,
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898,
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720
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],
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[
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956,
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629,
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576
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],
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[
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929,
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749,
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290
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],
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[
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604,
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841,
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296
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],
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[
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492,
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500,
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581
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],
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[
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561,
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179,
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502
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]
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],
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"max_edge_distance": 30
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}
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]

‎reproducibility/block_extraction/SGNsub_MLRN152L.json‎

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[
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{
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"cochlea": "M_LR_N152_L",
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"image_channel": [
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"CR",
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"Ntng1",
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"PV",
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"SGN_v2"
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],
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"segmentation_channel": "SGN_v2",
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"type": "sgn",
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"n_blocks": 6,
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"halo_size": [
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256,
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256,
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50
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],
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"component_list": [
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1,
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2
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],
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"crop_centers": [
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[
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791,
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1331,
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750
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],
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[
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752,
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997,
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849
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],
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[
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519,
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929,
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610
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],
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[
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794,
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904,
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420
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],
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[
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1013,
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613,
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479
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],
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[
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1013,
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330,
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643
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]
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],
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"max_edge_distance": 30
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}
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]

‎reproducibility/object_measures/SGNsubtype_MLR98L.json‎

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[
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{
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"cochlea": "M_LR_000098_L",
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"image_channel": [
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"PV",
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"CR",
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"Ntng1"
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],
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"segmentation_channel": "SGN_v2",
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"component_list": [
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1,
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2
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]
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}
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]

‎reproducibility/object_measures/SGNsubtype_MLRN152L.json‎

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[
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{
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"cochlea": "M_LR_N152_L",
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"image_channel": [
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"PV",
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"CR",
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"Ntng1"
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],
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"segmentation_channel": "SGN_v2",
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"component_list": [
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1,
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2
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]
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}
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]

‎reproducibility/tonotopic_mapping/2025-07-SGN_subtypes.json‎

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"cochlea": "M_AMD_N180_R",
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"segmentation_channel": "SGN_merged",
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"type": "sgn"
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},
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{
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"cochlea": "M_LR_N152_L",
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"segmentation_channel": "SGN_v2",
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"component_list": [
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1,
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2
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],
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"type": "sgn"
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},
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{
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"cochlea": "M_LR_000098_L",
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"segmentation_channel": "SGN_v2",
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"component_list": [
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1,
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2
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],
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"type": "sgn"
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}
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]

‎scripts/measurements/sgn_subtypes.py‎

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Original file line numberDiff line numberDiff line change
@@ -58,10 +58,14 @@ def frequency_mapping(frequencies, values, animal="mouse", transduction_efficien
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# "M_LR_000214_L": ["PV", "CR", "Calb1"],
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"M_LR_000184_R": ["PV", "Prph"],
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"M_LR_000184_L": ["PV", "Prph"],
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"M_LR_000098_L": ["PV", "CR", "Ntng1"],
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"M_LR_N152_L": ["PV", "CR", "Ntng1"],
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# "M_LR_000260_L": ["PV", "Prph", "Tuj1"],
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}
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COCHLEAE = {
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"M_LR_N152_L": {"seg_data": "SGN_v2", "subtype": ["CR", "Ntng1"], "component_list": [1, 2]},
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"M_LR_000098_L": {"seg_data": "SGN_v2", "subtype": ["CR", "Ntng1"], "component_list": [1, 2]},
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"M_LR_000099_L": {"seg_data": "PV_SGN_v2", "subtype": ["Calb1", "Lypd1"]},
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"M_LR_000184_L": {"seg_data": "SGN_v2", "subtype": ["Prph"], "output_seg": "SGN_v2b"},
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"M_LR_000184_R": {"seg_data": "SGN_v2", "subtype": ["Prph"], "output_seg": "SGN_v2b"},
@@ -71,7 +75,7 @@ def frequency_mapping(frequencies, values, animal="mouse", transduction_efficien
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REGULAR_COCHLEAE = [
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"M_LR_000099_L", "M_LR_000184_R", "M_LR_000184_L", # "M_LR_000260_L"
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"M_LR_000099_L", "M_LR_000184_R", "M_LR_000184_L", "M_LR_000098_L", "M_LR_N152_L" # "M_LR_000260_L"
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]
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# For custom thresholds.
@@ -300,7 +304,10 @@ def compile_data_for_subtype_analysis():
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table = pd.read_csv(table_content, sep="\t")
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# Get the SGNs in the main component
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table = table[table.component_labels == 1]
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component_list = [1]
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if "component_list" in list(COCHLEAE[cochlea].keys()):
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component_list = COCHLEAE[cochlea]["component_list"]
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table = table[table["component_labels"].isin(component_list)]
304311
print("Number of SGNs", len(table))
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valid_sgns = table.label_id
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@@ -315,7 +322,7 @@ def compile_data_for_subtype_analysis():
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)
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table_content = s3.open(os.path.join(table_folder, "default.tsv"), mode="rb")
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table = pd.read_csv(table_content, sep="\t")
318-
table = table[table.component_labels == 1]
325+
table = table[table["component_labels"].isin(component_list)]
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320327
# local
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table_name = f"{channel}_{seg_name.replace('_', '-')}_object-measures.tsv"

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