# Neural Depth morphology provenance

The collection contains 27 individual reconstructions: 24 neuronal forms and three glial forms. Two come from the Allen Cell Types Database and 25 from NeuroMorpho.Org. Twenty-five sources appear in one continuous comparative field; all 27 remain available in the Cell atlas. The developing Cajal-Retzius cell and cultured oligodendrocyte are atlas-only comparative specimens. This is a selective visual collection across regions, species, ages and preparation methods. It is not an exhaustive taxonomy, a representative census or a reconstructed biological circuit.

Labels follow the source records at different levels of granularity. A named morphology family is not necessarily a unique transcriptomic cell type. The original SWC files preserve recorded coordinates, compartment annotations, radii and parent relationships. No branches, somas, axons or synapses have been added to these source files.

Allen files were retrieved on 8 November 2026; NeuroMorpho files on 9 November 2026. The [manifest](./manifest.json) contains exact source and download URLs, original study DOIs, archive identities, byte counts, SHA-256 hashes, display projection and source caveats. Each record's `displayAnatomy` describes its source neighborhood, qualitative placement, field eligibility and any associated interpretation. This display metadata is separate from the original source region and preparation. Adjacent metadata JSON files preserve the corresponding official API records.

## Source collection

| Record | Source-defined form | Species | Source region | Recorded completeness | Study |
| --- | --- | --- | --- | --- | --- |
| [480114344](https://celltypes.brain-map.org/experiment/morphology/480114344) | Mouse layer 5 spiny pyramidal-type neuron | Mus musculus | Primary visual area, layer 5 | dendrite-only | Allen Cell Types Database |
| [341442651](https://celltypes.brain-map.org/experiment/morphology/341442651) | Mouse layer 2/3 Pvalb-line aspiny neuron | Mus musculus | Primary visual area, layer 2/3 | full | Allen Cell Types Database |
| [nmo-10069](https://neuromorpho.org/neuron_info.jsp?neuron_name=Purkinje-slice-ageP43-6) | Purkinje cell | mouse | cerebellum / cerebellar cortex / Purkinje layer | Dendrites Complete | [Original study](https://doi.org/10.1523/JNEUROSCI.2977-12.2013) |
| [nmo-32464](https://neuromorpho.org/neuron_info.jsp?neuron_name=195-4-7nj) | Cerebellar granule cell | clouded leopard | cerebellum / cerebellar cortex / stratum granulare / dorsal / right | Dendrites Moderate, Axon Incomplete | [Original study](https://doi.org/10.3389/fnana.2014.00024) |
| [nmo-61463](https://neuromorpho.org/neuron_info.jsp?neuron_name=140307-C1) | Cerebellar Golgi cell | mouse | cerebellum / cerebellar cortex / vermis | Dendrites Complete, Axon Incomplete | [Original study](https://doi.org/10.1016/j.neuron.2016.03.029) |
| [nmo-66828](https://neuromorpho.org/neuron_info.jsp?neuron_name=GlyT2_030_Slice3_Stellate_cell) | Cerebellar stellate cell | mouse | cerebellum / vermis | Dendrites Moderate, Axon Incomplete | [Original study](https://doi.org/10.1523/ENEURO.0055-16.2016) |
| [nmo-66825](https://neuromorpho.org/neuron_info.jsp?neuron_name=GlyT2_042_Slice4_Lugaro_cell-2) | Lugaro cell | mouse | cerebellum / vermis / granule layer | Dendrites Moderate, Axon Incomplete | [Original study](https://doi.org/10.1523/ENEURO.0055-16.2016) |
| [nmo-104452](https://neuromorpho.org/neuron_info.jsp?neuron_name=TT-04-03-14-1R) | Cortical basket cell | mouse | neocortex / medial prefrontal / layer 2 | Dendrites & Axon Moderate | [Original study](https://doi.org/10.1523/ENEURO.0208-18.2018) |
| [nmo-104461](https://neuromorpho.org/neuron_info.jsp?neuron_name=TT-12-18-13-1R) | Chandelier cell | mouse | neocortex / medial prefrontal / layer 2 | Dendrites & Axon Moderate | [Original study](https://doi.org/10.1523/ENEURO.0208-18.2018) |
| [nmo-130609](https://neuromorpho.org/neuron_info.jsp?neuron_name=2017-22-08-slice-2-cell-7-rotated) | Martinotti cell | mouse | neocortex / occipital / primary visual / layer 4 | Dendrites & Axon Complete | [Original study](https://doi.org/10.1038/s41467-019-12058-z) |
| [nmo-107156](https://neuromorpho.org/neuron_info.jsp?neuron_name=Fig2c_cell1_1402022rm) | Neurogliaform cell | human | neocortex / temporal / layer 1 | Dendrites & Axon Complete | [Original study](https://doi.org/10.1038/s41593-018-0205-2) |
| [nmo-130669](https://neuromorpho.org/neuron_info.jsp?neuron_name=2017-03-07-slice-2-cell-7-rotated) | Cortical bipolar interneuron | mouse | neocortex / occipital / primary visual / layer 4 | Dendrites & Axon Complete | [Original study](https://doi.org/10.1038/s41467-019-12058-z) |
| [nmo-61567](https://neuromorpho.org/neuron_info.jsp?neuron_name=L23BTC-j130221a-cell-7) | Bitufted interneuron | mouse | neocortex / occipital / primary visual / layer 2-3 | Dendrites Complete, Axon Moderate | [Original study](https://doi.org/10.1126/science.aac9462) |
| [nmo-7582](https://neuromorpho.org/neuron_info.jsp?neuron_name=double-bouquet) | Double-bouquet interneuron | rat | neocortex / frontal | Dendrites & Axon Complete | [Original study](https://doi.org/10.1038/srep00089) |
| [nmo-124344](https://neuromorpho.org/neuron_info.jsp?neuron_name=Anstoetz_NC_CajalRetzius_15) | Cajal-Retzius cell | mouse | neocortex / layer 1 | Dendrites & Axon Moderate | [Original study](https://doi.org/10.1007/s00429-013-0627-2) |
| [nmo-102095](https://neuromorpho.org/neuron_info.jsp?neuron_name=052417dgc1-1KS) | Dentate granule cell | mouse | hippocampus / dentate gyrus / granule layer / outer | Dendrites Complete | [Original study](https://doi.org/10.1016/j.neuroscience.2017.11.017) |
| [nmo-100](https://neuromorpho.org/neuron_info.jsp?neuron_name=n419) | CA1 pyramidal neuron | rat | hippocampus / CA1 | Dendrites Complete | [Original study](https://doi.org/10.1002/(SICI)1096-9861(19980216)391:3%3C335::AID-CNE4%3E3.0.CO;2-2) |
| [nmo-102974](https://neuromorpho.org/neuron_info.jsp?neuron_name=141012_Pair2DSGC) | Direction-selective retinal ganglion cell | mouse | retina | Dendrites Moderate, Axon Incomplete | [Original study](https://doi.org/10.1016/j.cub.2018.03.001) |
| [nmo-102946](https://neuromorpho.org/neuron_info.jsp?neuron_name=150501_pair1sac) | Starburst amacrine cell | mouse | retina | Dendrites Moderate | [Original study](https://doi.org/10.1016/j.cub.2018.03.001) |
| [nmo-130730](https://neuromorpho.org/neuron_info.jsp?neuron_name=18703cell3) | Thalamic relay neuron | mouse | thalamus / lateral geniculate nucleus / dorsal | Dendrites Moderate, Axon Incomplete | [Original study](https://doi.org/10.3389/fncel.2019.00426) |
| [nmo-111356](https://neuromorpho.org/neuron_info.jsp?neuron_name=TM6) | Olfactory mitral cell | mouse | main olfactory bulb / external plexiform layer / deep | Dendrites Moderate, Axon Incomplete | [Original study](https://doi.org/10.1038/s41598-018-25740-x) |
| [nmo-111355](https://neuromorpho.org/neuron_info.jsp?neuron_name=10ventrolateral_2T0925) | Olfactory tufted cell | mouse | main olfactory bulb / external plexiform layer / superficial | Dendrites Moderate, Axon Incomplete | [Original study](https://doi.org/10.1038/s41598-018-25740-x) |
| [nmo-252016](https://neuromorpho.org/neuron_info.jsp?neuron_name=04_02_2014_S4_C7_P21_traces) | Nigral dopaminergic neuron | rat | basal ganglia / substantia nigra / pars compacta | Dendrites Moderate, Axon Incomplete | [Original study](https://doi.org/10.1523/jneurosci.2331-21.2022) |
| [nmo-60996](https://neuromorpho.org/neuron_info.jsp?neuron_name=dSPN-Sham-A3S2N2) | Direct-pathway medium spiny neuron | mouse | basal ganglia / ventral striatum / nucleus accumbens / medial / shell | Dendrites Moderate | [Original study](https://doi.org/10.1038/nn.4199) |
| [nmo-131086](https://neuromorpho.org/neuron_info.jsp?neuron_name=Female-Control-Cell10) | Cultured oligodendrocyte | rat | neocortex | Process Complete | [Original study](https://doi.org/10.1002/glia.23799) |
| [nmo-106334](https://neuromorpho.org/neuron_info.jsp?neuron_name=wtsalF3068iba3_2) | Hippocampal microglia | mouse | hippocampus | Process Moderate | [Original study](https://doi.org/10.3389/fnmol.2018.00295) |
| [nmo-120143](https://neuromorpho.org/neuron_info.jsp?neuron_name=Ctx-GFAP-astro7) | Protoplasmic astrocyte | mouse | neocortex / somatosensory / primary somatosensory | Process Moderate | [Original study](https://doi.org/10.7554/eLife.45545) |

## Continuous composition

Scrolling travels through one persistent composite volume. Populations drawn from neocortex, hippocampus, thalamus, striatum, substantia nigra, cerebellum, olfactory bulb and retina contribute overlapping areas of visual influence. Their source identities remain distinct in the atlas, while the artwork has no scene gates or regional crossfades. This comparative arrangement spans species and preparations; its order, overlap and apparent depth do not map a continuous section through one brain or establish biological adjacency.

Somas occupy irregular positions around curved tissue surfaces or dispersed source neighborhoods. Directional cell families follow local surface orientation, retaining qualitative relationships such as apical arbors facing the superficial side. Depth varies continuously throughout the volume. Layer thickness, intercellular distances, apparent cell size, density and repeated instances are artistic choices, not anatomical measurements. The counts below identify distinct source reconstructions, not biological population proportions.

| Source neighborhood | Field sources | Placement and limits |
| --- | ---: | --- |
| Neocortex | 10 | Layer 1, layers 2/3, layer 4 and layer 5 sources keep qualitative depth ordering around curved surfaces. Pyramidal apical arbors face the local superficial side. Cortical basket and chandelier cells retain their cortical source context. The double-bouquet source has no specified layer and receives no numbered-layer assignment. Cortical areas and species remain comparative examples rather than one measured column. |
| Hippocampus | 3 | CA1 pyramidal and dentate granule populations retain distinct placement relationships around curved surfaces. CA1 apical and basal arbors keep their relative orientation; dentate dendrites face the molecular side. Microglia occupy interstitial space. No direct dentate-to-CA1 shortcut or missing CA3 population is drawn. |
| Thalamus | 1 | Mouse dorsal lateral geniculate relay cells form a dispersed nuclear population. No primate LGN layer scheme is imposed on this source. |
| Striatum | 1 | Nucleus accumbens shell medium spiny cells retain their own dispersed source neighborhood. Apparent overlap with other populations does not identify those cells as striatal residents. |
| Substantia nigra | 1 | The pars compacta dopaminergic reconstruction retains its own source neighborhood. The artwork does not reconstruct the nigrostriatal projection or assign dopaminergic output a simple excitatory category. |
| Cerebellum | 5 | Purkinje somata follow a narrow curved layer with dendritic fans oriented toward the local molecular side. Smaller, more numerous granule-cell instances and sparse Golgi cells lie beneath it. Lugaro somata sit just beneath the Purkinje layer with a tangential arbor orientation. Stellate cells occupy the molecular side by family interpretation, with the source annotation conflict disclosed below. |
| Olfactory bulb | 2 | Mitral somata occupy a qualitatively deeper position than the middle tufted-cell examples. The collection has no olfactory granule interneuron source and does not substitute cerebellar granule cells or imply a complete bulb microcircuit. |
| Retina | 2 | Ganglion and starburst arbors form an overlapping plexus viewed en face. This is not a retinal cross-section. No exact ON/OFF sublamina, complete retinal stack or recurrent ganglion-cell axon network is assigned. |

The local anatomical relationships are informed by the source records and primary anatomical work. [Kaneko et al., 2011](https://doi.org/10.1371/journal.pone.0020108) documents Purkinje dendritic planarity; [Eyre and Nusser, 2016](https://doi.org/10.1523/ENEURO.0055-16.2016) distinguishes cerebellar interneuron arbors and their laminar relationships. [Wheeler et al., 2015](https://doi.org/10.7554/eLife.09960) organizes hippocampal cell types by distinct areas and layers. The bulb source study, [Cavarretta et al., 2018](https://doi.org/10.1038/s41598-018-25740-x), distinguishes mitral and middle tufted populations. [Morrie and Feller, 2018](https://doi.org/10.1016/j.cub.2018.03.001) describes the overlapping radial starburst plexus. These references guide placement and orientation; they do not validate the artwork's coordinates or activity as measured anatomy.

### Development and culture

The Cell atlas retains two specimens outside the main neural field. The Cajal-Retzius source, `nmo-124344`, is a developing mouse cortical example with an age range of P7-11. The oligodendrocyte source, `nmo-131086`, comes from a P9 rat culture, recorded after four days in vitro, with planar process geometry. It is not used as an intact white-matter reconstruction and gains no invented myelin sheaths. Both source records, previews and original preparation metadata remain available.

## Drawing and activity

The renderer applies rigid viewing rotations to source coordinates, projects each view onto a plane, centers each reconstruction on its recorded soma, uniformly rescales it, and simplifies points along existing branch paths. A limited set of source-derived projection variants adds differences in viewpoint without bending branches or creating new biological specimens. The original files remain unmodified. Apparent size is staged from the recorded dendritic or glial-process footprint, so a long axon does not make its cell's dendrites artificially tiny. Relative size and orientation follow broad visual relationships, without claiming calibrated scale across sources or species. The continuous field compares reconstructions that would not normally be sampled together in one tissue section.

Directional cues use specific recorded compartments where available. The Martinotti source, `nmo-130609`, is oriented with its type-2 axonal centroid toward the superficial side. The mitral source, `nmo-111356`, uses a baseline YZ projection aligned to its recorded type-4 apical arbor, rather than its whole-arbor centroid. The tufted source, `nmo-111355`, has no annotated type-4 compartment. Its baseline YZ projection receives a rigid rotation of approximately -2.67779 radians, inferred from the compact 568-node terminal subtree rooted at original SWC node 1930. That subtree's soma-relative centroid is Y = 57.97525, Z = 115.90582 in the source coordinates. Additional viewing variants align to the same source subtree in their own projected coordinates. Interpreting it as the tuft guides display orientation only; no compartment labels, branches or source coordinates are changed.

The blue textures and the optional atlas thumbnails use the same original source geometry. Atlas thumbnails show the baseline projection; the field also uses rigid viewing variants of that geometry. Radii are drawn with bounded minimum and maximum line weights for legibility; records marked “No Diameter” do not establish measured branch thickness. A depicted soma is a schematic use of its recorded radius, not a membrane surface reconstruction.

Artificial short contacts connect selected recorded axon terminals to recorded dendritic arbors only within compatible source neighborhoods. The eligibility rules are deliberately conservative: they permit a limited set of cortical and cerebellar motifs, while omitting unsupported cross-region links, basket-cell distal-dendrite outputs, fabricated chandelier axon-initial-segment targets and generic recurrent meshes in nuclei, bulb or retina. The available source compartments further constrain which contacts can be drawn. Neither these contacts nor activity timing are measured data. Omitting a connection means the artwork does not model it, not that biology lacks that connection.

Disconnected source fragments remain visible, but only soma-connected paths can carry the illustrated propagation. Sources without a recorded axon do not acquire an invented axon. Coordinated word formation maps illustrated cell events to letter masks as an artistic interaction. A source with no recorded axon can contribute a timed field event to word formation without a fabricated axon or a source-to-letter cable. Sources with recorded axons can also drive visible artistic feeds into the lettering. Neither route is a hypothesis about language representation, a measured anatomical projection or a biophysical simulation.

The signal field records a broad physiological category only when supported by source labels or linked primary studies. “Unknown” is an unassigned visual activity category, not an assertion of excitation. These categories do not determine the sign of every biological synapse. Dopaminergic and dual-transmitter output are not forced into a binary physiological claim.

Glial reconstructions and the mature starburst amacrine cell are excluded from spike animation, neuronal contacts and spike-driven word recruitment. This does not mean those cells are biologically inactive. The starburst source uses graded signaling; see [Pottackal et al., 2021](https://pmc.ncbi.nlm.nih.gov/articles/PMC8351878/). Its presynaptic dendrites remain source geometry, without being converted into fabricated axons. The cultured oligodendrocyte is retained in the atlas only.

## Source-specific qualifications

The original Allen spiny source is labeled dendrite-only and includes a short, incomplete axon segment. The Pvalb-line source contains one soma-rooted tree and 83 separate axon fragments. These fragments remain separate. The original six Allen projection fingerprints are protected by regression checks.

NeuroMorpho record nmo-66828 has an unresolved layer annotation: its family and named reconstruction identify a stellate cell, while its region metadata includes granule layer. The source-region label remains the broader verified cerebellum / vermis, and the original annotation is preserved in the manifest and official metadata. Placement on the molecular side is an explicit interpretation of the verified stellate family, not a correction to the source record. [Eyre and Nusser, 2016](https://doi.org/10.1523/ENEURO.0055-16.2016) and [Ma et al., 2020](https://pmc.ncbi.nlm.nih.gov/articles/PMC7459332/) support the stellate family assignment; the latter explicitly uses this named reconstruction. The conflict is disclosed in the atlas instead of silently reclassifying the cell.

The repository's completeness labels describe each reconstruction, not complete preservation of every in-vivo process. “No Axon” means no axon compartment was included in that trace. It does not establish that the entire cell class lacks an axon. The collection includes a clouded-leopard cerebellar granule cell and a human cortical neurogliaform cell; both are labeled by species rather than presented as mouse or human-brain equivalents.

## Rights and attribution

### Allen Institute

Allen Institute for Brain Science. *Allen Cell Types Database*. Specimens [480114344](https://celltypes.brain-map.org/experiment/morphology/480114344) and [341442651](https://celltypes.brain-map.org/experiment/morphology/341442651). Accessed 8 November 2026.

These two files retain the [Allen Institute Terms of Use](https://alleninstitute.org/legal/terms-of-use), including their research/noncommercial-use conditions. They are not relicensed as Creative Commons or under this application's software license. Original notices remain intact. The [Allen Citation Policy](https://alleninstitute.org/legal/citation-policy) requires discoverable attribution on the same page as the data; the homepage's Cell atlas includes both specimen links and attribution. No endorsement is implied.

### NeuroMorpho.Org

The 25 additional reconstructions are from **NeuroMorpho.Org (RRID:SCR_002145)** under [Creative Commons Attribution 4.0](https://creativecommons.org/licenses/by/4.0/). The repository's [reuse terms](https://neuromorpho.org/useterm.jsp) require credit to the original studies, the repository and the following publication:

Tecuatl C, Ljungquist B, Ascoli GA (2024). *Accelerating the continuous community sharing of digital neuromorphology data*. FASEB Bioadv. 6(7):207-221. [doi:10.1096/fba.2024-00048](https://doi.org/10.1096/fba.2024-00048).

Original studies are linked for each source above, in the manifest and in the Cell atlas. Visual adaptations are by Arzola Research. The original SWCs are unchanged; display projection, path simplification, color, line weights and composition are the adaptations.

Programmatic retrieval used NeuroMorpho's official API and direct standardized-SWC download URLs, with an identifying user agent. No detail-page scraping was used to collect the data.

## Delivery and reproducibility

The original source files total 7,765,562 bytes. Byte-exact gzip delivery copies total 2,434,927 bytes. Gzip changes transfer encoding, not source geometry. Browsers with native streaming decompression load the compressed copies; other browsers, or failed compressed transfers, use the original SWCs.

Run `node scripts/prepare-neural-morphology.mjs` to regenerate gzip copies and source-derived SVG thumbnails. It checks each raw source digest before creating a derivative. Run `node scripts/verify-neural-morphology.mjs` to check identities, compressed-file digests, exact decompression, source topology, metadata consistency and render geometry. Zero radii and disconnected fragments are retained when present; the checks do not repair source anatomy by inventing connections.