Archive MaleCNS research sources, provenance, bibliography and immutable data inventory
This commit is contained in:
Digital Drosophila Archive
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||||
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"vic",
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||||
"area_fit",
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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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||||
],
|
||||
"url": "https://github.com/reiserlab/celltype-explorer-drosophila-male-cns"
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||||
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||||
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||||
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|
||||
"/data/digital-drosophila/experiments/phase4f-retinotopic-vision/external-resources/visualpathways/LICENSE"
|
||||
],
|
||||
"url": "https://github.com/reiserlab/visualpathways"
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||||
}
|
||||
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|
||||
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||||
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Load Diff
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phase: 4F
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||||
names:
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||||
reference: MaleCNS-LIF-reference-v1
|
||||
runtime: MaleCNS-LIF-runtime-v1
|
||||
io_api: MaleCNS-BrainIO-v1
|
||||
activity_stream: MaleCNS-ActivityStream-v1
|
||||
encoder: MaleCNS-VisualEncoder-v1
|
||||
candidate: MaleCNS-VisualEncoder-v1-candidate
|
||||
|
||||
paths:
|
||||
connectome_root: /data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only
|
||||
model_root: /data/digital-drosophila/models/male-cns-lif
|
||||
reference_root: /data/digital-drosophila/models/male-cns-lif/reference-v1
|
||||
runtime_root: /data/digital-drosophila/models/male-cns-lif/runtime-v1
|
||||
io_root: /data/digital-drosophila/models/male-cns-lif/io-v1
|
||||
phase4c_root: /data/digital-drosophila/experiments/phase4c-runtime
|
||||
phase4d_root: /data/digital-drosophila/experiments/phase4d-io
|
||||
phase4e_root: /data/digital-drosophila/experiments/phase4e-visual-calibration
|
||||
experiment_root: /data/digital-drosophila/experiments/phase4f-retinotopic-vision
|
||||
encoder_root: /data/digital-drosophila/models/male-cns-lif/visual-encoder-v1
|
||||
external_root: /data/digital-drosophila/experiments/phase4f-retinotopic-vision/external-resources
|
||||
|
||||
device:
|
||||
required_name_substring: RTX 4090
|
||||
launcher_visible_gpu_uuid: GPU-79f3a85d-adce-7833-7003-6488140ca596
|
||||
|
||||
model:
|
||||
dt_ms: 0.1
|
||||
membrane_tau_ms: 20.0
|
||||
synaptic_tau_ms: 5.0
|
||||
refractory_ms: 2.2
|
||||
resting_potential_mv: -52.0
|
||||
reset_potential_mv: -52.0
|
||||
threshold_mv: -45.0
|
||||
synaptic_delay_ms: 1.8
|
||||
w_syn_mv_per_anatomical_synapse: 0.275
|
||||
|
||||
sign_policy:
|
||||
neurotransmitter_sign: {acetylcholine: 1, gaba: -1, glutamate: -1, dopamine: 1, octopamine: 1, serotonin: 1, histamine: -1}
|
||||
unknown_sign: 0
|
||||
unclear_sign: 0
|
||||
|
||||
official_resources:
|
||||
visualpathways_commit: 23f6ac131529b5f56894c6eeb9b88b17894fc00d
|
||||
celltype_explorer_commit: 789cc6c105798ce2fd70ba85dab394f90899616b
|
||||
flyvis_commit: 92b3845cc426dd309a1a0e1b3890156c42e14021
|
||||
retinotopy_tbar_url: https://storage.googleapis.com/flyem-male-cns/auxiliary-data/retinotopy-tbars/retinotopy_tbar_olr-2026-06-26.precomputed
|
||||
paper_doi: 10.1016/j.cell.2026.08.014
|
||||
|
||||
encoder:
|
||||
trial_duration_ms: 100.0
|
||||
temporal_segments: 5
|
||||
targets_per_segment: 460
|
||||
poisson_rate_hz: 50.0
|
||||
external_drive_mv: 8.8
|
||||
seeds: [46101, 46102, 46103]
|
||||
flyvis_bridge:
|
||||
geometry: regular axial hex lattice sized from official MaleCNS unique eye columns
|
||||
coordinate_equations: exact public flyvis.utils.hex_utils get_hex_coords/hex_to_pixel default convention
|
||||
channel_weights: {luminance: 1.0, on_change: 1.0, off_change: 1.0, temporal_motion: 0.5, horizontal_motion_tendency: 1.0, vertical_motion_tendency: 1.0}
|
||||
target_expression: annotation_superclass in [visual_projection, visual_projection_tbc] with retinotopic coordinate
|
||||
patterns:
|
||||
- full-field
|
||||
- left-spot
|
||||
- right-spot
|
||||
- upper-spot
|
||||
- lower-spot
|
||||
- left-to-right
|
||||
- right-to-left
|
||||
- up-to-down
|
||||
- down-to-up
|
||||
- looming
|
||||
- sparse-moving-object
|
||||
- static-object
|
||||
matched_pairs:
|
||||
- [left-spot, right-spot]
|
||||
- [upper-spot, lower-spot]
|
||||
- [left-to-right, right-to-left]
|
||||
- [up-to-down, down-to-up]
|
||||
- [looming, left-to-right]
|
||||
- [sparse-moving-object, static-object]
|
||||
runaway: {active_fraction_gte: 0.80, mean_firing_rate_hz_gte: 100.0, peak_step_fraction_gte: 0.10}
|
||||
|
||||
success_gate:
|
||||
minimum_separable_matched_pairs_in_descending_or_motor: 2
|
||||
minimum_graph_hops: 2
|
||||
maximum_output_latency_ms: 100.0
|
||||
require_non_runaway: true
|
||||
require_frozen_regression: true
|
||||
|
||||
readout:
|
||||
bins_ms: [1, 5, 10, 20, 50]
|
||||
|
||||
regression:
|
||||
float_absolute_tolerance: 0.00390625
|
||||
reference_trials:
|
||||
- {name: auditory-10hz, population: auditory, rate_hz: 10, seed: 42001, duration_ms: 1000.0}
|
||||
- {name: auditory-100hz, population: auditory, rate_hz: 100, seed: 42001, duration_ms: 1000.0}
|
||||
- {name: olfactory-50hz, population: olfactory, rate_hz: 50, seed: 42003, duration_ms: 1000.0}
|
||||
- {name: mechanosensory-50hz, population: mechanosensory, rate_hz: 50, seed: 42003, duration_ms: 1000.0}
|
||||
- {name: gustatory-50hz, population: gustatory, rate_hz: 50, seed: 42003, duration_ms: 1000.0}
|
||||
|
||||
prohibitions:
|
||||
connectome_changes: false
|
||||
raw_weight_changes: false
|
||||
lif_semantics_changes: false
|
||||
transmitter_sign_changes: false
|
||||
brain_gain_changes: false
|
||||
training: false
|
||||
reinforcement_learning: false
|
||||
game_integration: false
|
||||
action_decoder: false
|
||||
web_server: false
|
||||
three_d_frontend: false
|
||||
phase4g: false
|
||||
File diff suppressed because it is too large
Load Diff
+2738
File diff suppressed because it is too large
Load Diff
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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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||||
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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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|
||||
+130
@@ -0,0 +1,130 @@
|
||||
{
|
||||
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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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|
||||
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||||
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|
||||
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|
||||
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|
||||
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"readout_modes_passed": true,
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},
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"trials": {
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"passed": true,
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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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|
||||
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|
||||
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||||
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|
||||
"passed": true,
|
||||
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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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|
||||
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|
||||
"passed": true,
|
||||
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|
||||
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|
||||
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|
||||
"wall_seconds": 11.493563333002385
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,36 @@
|
||||
{
|
||||
"canonical_neurons": 166700,
|
||||
"connectome_derived_projection": 6618,
|
||||
"coordinate_kind_counts": {
|
||||
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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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|
||||
"mapped_total_including_connectome_derived": 30398,
|
||||
"normalization": {
|
||||
"hex1_min_max": [
|
||||
1.0,
|
||||
36.0
|
||||
],
|
||||
"hex2_min_max": [
|
||||
1.0,
|
||||
39.0
|
||||
],
|
||||
"method": "independent min-max of preserved official-equivalent hex coordinates to [-1,1]",
|
||||
"no_cartesian_claim": true
|
||||
},
|
||||
"official_annotation_both_coordinates": 23720,
|
||||
"official_tbar_canonical_bodies": 9,
|
||||
"official_tbar_unique_bodies": 580,
|
||||
"reliable_official_coordinate_coverage_percent": 14.265146970605878,
|
||||
"reliable_official_coordinate_neurons": 23780,
|
||||
"schema": "body_id: uint64\nneuron_idx: int32\nvisual_layer: string\ncell_type: string\ninstance: string\nside: string\nneurotransmitter: string\nofficial_hex1: double\nofficial_hex2: double\nretinotopic_x: double\nretinotopic_y: double\ncoordinate_kind: string\ncoordinate_reliability: string\nvisual_input_contribution: double\nreceptive_field_r: double\nreceptive_field_theta: double\nreceptive_field_vic: double\npathway_class: string\npathway_class_source: string\nprovenance: string\neye: string\neye_map_cell_type: string\n-- schema metadata --\npandas: '{\"index_columns\": [], \"column_indexes\": [], \"columns\": [{\"name\":' + 2897",
|
||||
"table": "/data/digital-drosophila/experiments/phase4f-retinotopic-vision/retinotopy/visual-retinotopy.parquet",
|
||||
"visual_projection_mapped": 6618,
|
||||
"visual_projection_total": 9203,
|
||||
"visualpathways_eye_map_canonical_rows": 23758
|
||||
}
|
||||
+2090
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user