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Added subtype cochleae: N110L, N110R
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+227
-6
lines changed

10 files changed

+227
-6
lines changed

‎reproducibility/block_extraction/SGNsub_MAMDRunx1L.json‎

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[
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{
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"cochlea": "M_AMD_Runx1_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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"PV_SGN_v2"
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],
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"segmentation_channel": "PV_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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],
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"crop_centers": [
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[
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945,
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1155,
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571
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],
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[
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830,
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],
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[
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808,
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966,
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870
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],
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[
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555,
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1130,
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840
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],
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[
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357,
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1024,
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611
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],
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[
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176,
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748,
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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_MLRN110L.json‎

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[
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{
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"cochlea": "M_LR_N110_L",
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"image_channel": [
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"Calb1",
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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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],
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"crop_centers": [
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[
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653,
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1124,
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730
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],
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[
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840,
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887,
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878
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],
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[
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594,
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611,
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870
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],
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[
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],
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[
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],
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[
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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_MLRN110R.json‎

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[
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{
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"cochlea": "M_LR_N110_R",
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"image_channel": [
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"Calb1",
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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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],
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"crop_centers": [
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[
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1149,
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1090,
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453
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],
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[
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1104,
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900,
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724
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],
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[
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741,
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900,
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692
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],
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[
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],
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[
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954,
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],
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[
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922,
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154,
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703
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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_MAMDRunx1L.json‎

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{
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"cochlea": "M_AMD_Runx1_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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],

‎reproducibility/object_measures/SGNsubtype_MLRN110L.json‎

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[
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{
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"cochlea": "M_LR_N110_L",
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"image_channel": [
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"PV",
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"Calb1",
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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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]
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}
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]

‎reproducibility/object_measures/SGNsubtype_MLRN110R.json‎

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[
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{
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"cochlea": "M_LR_N110_R",
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"image_channel": [
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"PV",
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"Calb1",
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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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]
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}
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]

‎reproducibility/tonotopic_mapping/2025-07-SGN_subtypes.json‎

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"segmentation_channel": "PV_SGN_v2",
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"type": "sgn"
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},
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{
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"cochlea": "M_LR_000214_L",
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"segmentation_channel": "PV_SGN_v2",
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"type": "sgn"
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},
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{
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"cochlea": "M_LR_000214_L",
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"segmentation_channel": "PV_SGN_v2",
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"type": "sgn"
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},
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{
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"cochlea": "M_AMD_N180_L",
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"segmentation_channel": "SGN_merged",
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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_N110_L",
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"segmentation_channel": "SGN_v2",
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"type": "sgn"
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},
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{
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"cochlea": "M_LR_N110_R",
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"segmentation_channel": "SGN_v2",
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"type": "sgn"
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}
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]

‎scripts/assign_subtypes.py‎

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# from skimage.segmentation import relabel_sequential
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COCHLEA_DICT = {
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"M_LR_000098_L": {"seg_data": "SGN_v2", "subtype": ["CR", "Ntng1"]},
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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_v2b", "subtype": ["Prph"]},
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"M_LR_000184_R": {"seg_data": "SGN_v2b", "subtype": ["Prph"]},
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"M_LR_000260_L": {"seg_data": "SGN_v2", "subtype": ["Prph", "Tuj1"]},
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"M_LR_N152_L": {"seg_data": "SGN_v2", "subtype": ["CR", "Ntng1"]},
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"M_AMD_N180_L": {"seg_data": "SGN_merged", "subtype": ["CR", "Ntng1"]},
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"M_AMD_N180_R": {"seg_data": "SGN_merged", "subtype": ["CR", "Ntng1"]},
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}

‎scripts/export_lower_resolution_subtypes.py‎

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"M_LR_000184_L": {"seg_data": "SGN_v2b", "subtype": ["Prph"]},
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"M_LR_000184_R": {"seg_data": "SGN_v2b", "subtype": ["Prph"]},
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"M_LR_000260_L": {"seg_data": "SGN_v2", "subtype": ["Prph", "Tuj1"]},
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"M_LR_N152_L": {"seg_data": "SGN_v2", "subtype": ["CR", "Ntng1"]},
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}
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# Prph is isolated.
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"Prph+": "Type II",
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"Prph-": "Type I",
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# Combinations of CR and Ntng1
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"CR+/Ntng1+": "Type Ib",
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"CR+/Ntng1-": "Type Ia",
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"CR-/Ntng1+": "Type Ic",
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"CR-/Ntng1-": "inconclusive",
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}
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‎scripts/measurements/sgn_subtypes.py‎

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@@ -61,9 +61,15 @@ def frequency_mapping(frequencies, values, animal="mouse", transduction_efficien
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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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"M_LR_N110_L": ["PV", "Calb1", "Ntng1"],
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"M_LR_N110_R": ["PV", "Calb1", "Ntng1"],
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"M_AMD_Runx1_L": ["PV", "CR", "Ntng1"],
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}
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COCHLEAE = {
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"M_LR_N110_L": {"seg_data": "SGN_v2", "subtype": ["Calb1", "Ntng1"]},
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"M_LR_N110_R": {"seg_data": "SGN_v2", "subtype": ["Calb1", "Ntng1"]},
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"M_AMD_Runx1_L": {"seg_data": "SGN_v2", "subtype": ["CR", "Ntng1"]},
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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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REGULAR_COCHLEAE = [
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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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"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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"M_LR_N110_L", "M_LR_N110_R", "M_AMD_Runx1_L",
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]
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# For custom thresholds.
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# For consistent colors.
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ALL_COLORS = ["red", "blue", "orange", "yellow", "cyan", "magenta", "green", "purple", "gray", "black"]
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COLORS = {
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"Type Ia": "#133374",
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"Type Ib": "#27339C",
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"Type Ib/Ic": "#67279C",
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"Type Ic": "#9C276F",

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