ybb2297/CIC_Morph

Hippocampal formation single-neuron reconstructions, compartment-labeled

8,321 mouse single-neuron reconstructions from the hippocampal formation (CA1, CA2, CA3, DG, PARA, POST, PRE), registered to the Allen CCFv3. Every node has been labeled by compartment: soma, axon, basal dendrite or apical dendrite.

A separate section, saustad2026_SUB/, adds the 689 subicular reconstructions from Saustad et al. (2026). Those files keep the authors' original node types, and their labels are the authors' column, layer and class (see below).

Quick start

One region, no code: download the zip you need from zips/, for example zips/CA1_full_morph.zip. Each zip holds the SWCs, their change logs and a metadata.csv for that group.

Python:

from huggingface_hub import snapshot_download
import pandas as pd

repo = "ybb2297/CIC_Morph"
meta = pd.read_csv(f"hf://datasets/{repo}/metadata.csv")

# only CA1 full morphologies
path = snapshot_download(repo, repo_type="dataset", allow_patterns=["swc/CA1/full_morph/*"])

Layout

metadata.csv                        one row per neuron (start here)
summary_by_region.csv               counts per region / type
swc/<REGION>/<type>/<id>.swc        labeled reconstructions
change_logs/<REGION>/<type>/<id>_change_log.csv
zips/<REGION>_<type>.zip            same files, one archive per group
zips/saustad2026_SUB.zip
saustad2026_SUB/
  metadata.csv                      authors' column / layer / class / targets per neuron
  swc/<column>/<id>.swc

<type> is full_morph or projections:

• full_morph: complete morphologies (axon and dendrites), labeled by hand.
• projections: projection-only reconstructions. The root is the soma (type 1) and every other node is axon (type 2).

Contents

Neurons per region. Every cell in the labeled set is compartment-labeled; "QC ok" means no unlabeled nodes remain (see qc_flag).

Region	Full morphology	Projection-only	Total neurons	With change log	QC ok
CA1	1,477	2,216	3,693	3,551	3,043
CA2	47	—	47	45	38
CA3	471	425	896	836	748
Dentate gyrus (DG)	1,326	1,733	3,059	2,169	2,594
Parasubiculum (PARA)	129	—	129	101	88
Postsubiculum (POST)	168	—	168	116	113
Presubiculum (PRE)	329	—	329	221	204
Labeled set total	3,947	4,374	8,321	7,039	6,828
Subiculum (SUB), Saustad et al.	689	—	689	—	—
All neurons	4,636	4,374	9,010

Saustad et al. subicular neurons by the authors' column and class:

Column	Neurons	IT	ET	CT
SUBdd	167	137	0	30
SUBdv	83	64	0	19
ProSUB	111	0	59	52
SUBv	273	40	138	95
SUBvv	55	33	12	10
Total	689	274	209	206

File format

Standard SWC, with seven whitespace-separated columns: id type x y z radius parent. Coordinates are Allen CCFv3 micrometres in axis order AP, DV, ML. The root has parent -1.

type	meaning
1	soma
2	axon
3	basal dendrite
4	apical dendrite
0, 10–12	unlabeled (only in cells flagged below, and in the Saustad section)

Change logs record every type change made during labeling, relative to the original reconstruction. Columns: node_id, old_type, new_type, scope, root_id. The 1,258 older logs have no root_id column. A cell has no log when labeling did not change any node type.

metadata.csv

column	meaning
neuron_id	brain_cell id, e.g. 202254_016
region, morph_type	folder the cell sits in
swc_path, change_log_path	relative paths (empty if no log)
n_nodes, n_soma, n_axon, n_basal, n_apical, n_unlabeled	node counts per type
n_roots	number of root nodes. Cells with more than one root are reconstructions with separate fragments (multi_fragment, 55 cells)
n_type_changes	nodes whose type differs from the original reconstruction
source_batch, source_set	labeling batch and set the cell came from
qc_flag	ok (6,828), minor_unlabeled (1,485: a few nodes left unlabeled, almost always well under 1% of the cell), needs_relabel (8: labeling incomplete; exclude them for compartment-level analyses)

Saustad et al. subicular set (saustad2026_SUB/)

689 subicular neurons from Saustad et al., Mapping Projectome Heterogeneity of Subiculum Neuron Cell Types (Hippocampus, 2026). The files are in the same CCFv3 frame and axis order as the main set. The two sets share no neuron ids.

• Node types are the authors' originals and are not compartment-labeled. About 69% of nodes are type 0, 28% axon and 4% basal dendrite.
• metadata.csv columns:
  • column: the authors' subdivision. SUBdd 167, SUBdv 83, ProSUB 111, SUBv 273, SUBvv 55.
  • sub_layer: the authors' layer, 1–4.
  • cls: class derived from the layer. Layers 1–2 are IT (274), layer 3 is ET (209), layer 4 is CT (206).
  • targets, n_targets: the authors' projection targets.
  • Node counts per type, as in the main metadata.
• Membership and labels come from the Neuron_IDs sheet of the authors' spreadsheet. Nothing has been relabeled.

Paper: https://onlinelibrary.wiley.com/doi/10.1002/hipo.70138 (doi: 10.1002/hipo.70138)

Please cite Saustad et al. (2026) when you use this section, and see the paper for methods, definitions and data availability. The license terms of the original authors apply.

License

CC BY-NC 4.0 for the labeled set. The Saustad et al. section is redistributed under its authors' terms.