Finger Pathway Atlas · V3 / V4 references

Model and real tissue

50 comparison plates · 42 original figures · 19 studies and the H01 gallery

Left: the supplied V3 model, retained as the development baseline. Right: published scientific tissue images used to guide V4 morphology. These plates are not V4 screenshots. The two panels have independent magnifications and represent different specimens, fields and scales. Source species and imaging methods are identified on every plate.

M1, S1 and the six-layer cortical sections

Open the paired coronal sections →. Both gyri remain visible at a shared physical zoom. The body view displays only the left precentral and postcentral gyri. The paired inspection panels use separate anterior–posterior planes: they are modeled MRI-style tissue sections, not a patient scan or a single slice placing M1 and S1 next to each other.

M1 uses a 3.4 mm cortical thickness prior, a thin layer IV and an expanded layer V; S1 uses a 2.2 mm prior and a more prominent granular IV. These numerical fractions, cell counts and placements are construction parameters. Layer VI follows the gray–white boundary and contains separate soma-connected corticothalamic projection examples. The M1 corticospinal examples originate in V. A continuation below the section means “axon continues,” not a measured synapse or a reconstructed thalamic endpoint.

Shapson-Coe et al. (2024), A petavoxel fragment of human cerebral cortex reconstructed at nanoscale resolution. Human temporal-cortex ultrastructure and laminar reference. Official H01 data and CC BY 4.0 license; layer distributions. H01 is not M1 or S1. V4 imports twelve connected proofread neurite trees, two per source layer, then makes separately identified morphology transplants in the two regions. It does not replicate H01’s complete volume or connectivity.
García-Cabezas & Barbas (2014), Area 4 has layer IV in adult primates. Rhesus histology supports a thin, sparsely populated M1 IV and prevents falsely removing that layer. The model’s human layer fractions are not measurements from these animals.
Location of the central sulcus via cortical thickness of the precentral and postcentral gyri on MR (1996). MRI evidence for the relative thickness difference used to distinguish the gyri; not a source segmentation for these meshes.
Thalamocortical and the dual pattern of corticothalamic projections of the posterior parietal cortex in macaque monkeys (2007). Tracing evidence distinguishes layer-VI and layer-V corticothalamic projection patterns; used as a cross-area primate connectional reference, not direct proof of individual human M1/S1 endpoints.

How DKI should guide the axon tracts

Use diffusion MRI to constrain the local orientation distribution of a bundle. Fit diffusion and kurtosis tensors to suitable multi-shell diffusion data after motion, distortion and gradient corrections. Estimate the kurtosis diffusion orientation distribution, retain credible directional peaks, and integrate trajectories with stated curvature, step-size and tissue-mask rules. Register the result to cortical gray–white surfaces in physical coordinates. The 3D rendering then sweeps a cylindrical surface along each modeled path; radius is a separate histological prior.

V4 currently uses anatomical trajectory priors; it has not fitted DKI data. DKI does not identify single axons, their physical diameters, one-to-one cell attachments or synapses. Multiple paths must remain separate at crossings; streamlines must not merge into an artificial common neuron. Do not interpret a streamline count as an axon count. The displayed sparse fiber spacing is a rendering/sample choice, not a DKI measurement.

Jensen et al. (2005), Diffusional kurtosis imaging: The quantification of non-Gaussian water diffusion by means of magnetic resonance imaging. Basis of the non-Gaussian diffusion expansion.
Jensen, Helpern & Tabesh (2014), Leading non-Gaussian corrections for diffusion orientation distribution function. Uses diffusion and kurtosis tensors to estimate orientations, including crossing bundles.
Glenn et al. (2015), Optimization of white matter fiber tractography with diffusional kurtosis imaging. Reproducibility, efficient orientation estimation and handling of nonphysical negative ODF values.
Glenn et al. (2016), Mapping the Orientation of White Matter Fiber Bundles. Comparison of DTI, DKI and DSI orientation estimates.
Fieremans, Jensen & Helpern (2011), White matter characterization with diffusional kurtosis imaging. Compartment modeling under restricted assumptions, including approximately aligned bundles; not a general individual-axon diameter estimator.

H01 source IDs, physical coordinates, radii and provenance. The source SWC coordinates were verified against original H01 skeleton coordinates. Connected neurite topology is retained with a 0.7 µm centerline simplification tolerance. Cylindrical radius approximates the source skeleton, not the original EM membrane surface. The visible-fiber option widens display radius; switch it off to use physical diameter.

01 · Skin & sensory endings

A Meissner corpuscle in human fingertip skin

Human · Histology
Fingertip; cadaveric skin

Compare the terminal-bearing corpuscle with its surrounding dermal papilla, not only the outer outline.

Model differences and attribution

The model is much more regular and isolated; surrounding cells and papillary attachment are simplified.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Kim & Lee, 2020 — Figure 1A; fingertip

Copyright © 2020. Anatomy & Cell BiologyThis is an open-access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Source license

02 · Skin & sensory endings

Meissner afferents: reconstructed terminal topology

Mouse · EM reconstruction
Glabrous skin; Meissner corpuscle

The reference separates two traced afferents and shows a highly folded terminal contour.

Model differences and attribution

The modeled repeating loops are a visual placeholder, not the reconstructed arbor shown at right.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Handler et al., 2023 — Figure 6A-B; traced afferents with orientation drawings

The source retains its copyright and reuse terms; consult the original publication.

03 · Skin & sensory endings

Meissner supporting lamellae and axon relationships

Mouse · EM reconstruction
Glabrous skin; Meissner corpuscle

Compare the relative positions of axon and supporting cells across the reconstructed corpuscle.

Model differences and attribution

The model uses repeated flattened shells; real lamellar cells need individual boundaries and nonuniform contacts.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Handler et al., 2023 — Figure 6C; supporting cells and colored EM sections

The source retains its copyright and reuse terms; consult the original publication.

04 · Skin & sensory endings

Meissner corpuscles in an electron-microscope section

Mouse · Electron microscopy
Digit-tip Meissner corpuscles; genetically labeled endings

The two source sections expose irregular axonal profiles among closely packed lamellae.

Model differences and attribution

This is a section-versus-surface comparison. A 3D outer shell cannot substitute for the internal section pattern.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Neubarth et al., 2020 — Figure 6B; TrkB and Ret labeling

The source retains its copyright and reuse terms; consult the original publication.

05 · Skin & sensory endings

Meissner terminal ultrastructure

Mouse · Electron microscopy
Digit-tip Meissner corpuscles

Inspect the gap between a smooth modeled membrane and organelle-containing, closely apposed tissue.

Model differences and attribution

Mitochondria, membrane junctions, and the source-specific supporting-cell arrangement are not modeled.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Neubarth et al., 2020 — Figure 6C; terminal close-ups

The source retains its copyright and reuse terms; consult the original publication.

06 · Skin & sensory endings

Merkel complexes in an intact touch dome

Mouse · Immunofluorescence
Hairy-skin touch dome; not a glabrous fingertip

Compare a branching afferent contacting several Merkel-cell profiles with the labeled cellular cluster.

Model differences and attribution

The tissue site differs. The model lacks the measured cluster geometry and surrounding keratinocyte boundaries.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Hoffman et al., 2018 — Figure 1E; whole-mount touch dome

The source retains its copyright and reuse terms; consult the original publication.

07 · Skin & sensory endings

The Pacinian organ and its reconstructed sensory ending

Mouse · Tomography + EM reconstruction
Pacinian corpuscle near fibula; not a human finger

Compare the organ envelope and long central ending while keeping the two imaging modalities distinct.

Model differences and attribution

The model shows an idealized capsule. It does not reproduce the traced terminal protrusions or exact inner-core anatomy.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Handler et al., 2023 — Figure 7A; whole-organ context

The source retains its copyright and reuse terms; consult the original publication.

08 · Skin & sensory endings

Pacinian terminal protrusions and inner-core contact

Mouse · EM reconstruction
Fibular Pacinian corpuscle

The reference resolves terminal surface projections that disappear in a smooth capsule-based representation.

Model differences and attribution

The side-on V3 cutaway still obscures much of the central ending; its inner-core microgeometry needs rebuilding.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Handler et al., 2023 — Figure 7B; terminal region

The source retains its copyright and reuse terms; consult the original publication.

09 · Skin & sensory endings

Pacinian lamellar Schwann cells are complex individual cells

Mouse · EM reconstruction
Fibular Pacinian inner core

Compare repeated modeled lamellae with individually reconstructed, interleaved supporting cells.

Model differences and attribution

One nested shell per layer is not equivalent to one real Schwann cell; topology and contacts remain missing.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Chen et al., 2025 — Figure 1B-C; individual lamellar Schwann cells and axon

Copyright © 2025 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY).This is an open-access article distributed under the terms of the Creative Commons Attribution license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Source license

10 · Skin & sensory endings

Axon-to-lamellar-cell contact sites

Mouse · EM reconstruction
Pacinian inner core

The source explicitly locates contacts on the axon body and its protrusions.

Model differences and attribution

No measured cell-to-cell contact map is encoded in the V3 Pacinian specimen.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Chen et al., 2025 — Figure 2B-C; axon body and protrusions

Source license

11 · Skin & sensory endings

Pacinian support-cell junctions at nanometer scale

Mouse · Electron microscopy
Pacinian lamellar cells

These micrographs show the level of membrane detail absent from an organ-scale surface model.

Model differences and attribution

This is an ultrastructure target, not a claim that such junctions are presently visible or simulated.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Chen et al., 2025 — Figure 3; lower EM junction panels

Source license

12 · Skin & sensory endings

Free nerve endings in healthy human skin

Human · Immunofluorescence
Healthy volunteer skin biopsy; lower-limb site

Compare irregular fine branches crossing skin layers with the model’s unencapsulated arbor.

Model differences and attribution

The model does not reproduce the actual epidermal trajectory, varicosities, or fiber density of this biopsy.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Van Acker et al., 2016 — Figure 3; PGP9.5 staining

© The Author(s). 2016https://creativecommons.org/licenses/by/4.0/ Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Source license

13 · Skin & sensory endings

Varicose epidermal fibers in human sole skin

Human · Immunohistology
Sole skin; not fingertip skin

The source makes the bead-like changes along very fine epidermal fibers visible.

Model differences and attribution

V3 has comparatively smooth fine branches. Sole and fingertip specimens should not share an unqualified density prior.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Wu et al., 2024 — Figure 2B-G; epidermal fibers and varicosities

14 · Skin & sensory endings

Human epidermal fibers reconstructed from label-free signals

Human · Optical reconstruction
Ex vivo sole skin

Compare the 3D course of signal-defined fibers with the model’s branching tree.

Model differences and attribution

This optical reconstruction is not EM membrane segmentation; neither panel is a complete epidermal connectome.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Wu et al., 2024 — Figure 3N-Q; projection and 3D views

15 · Peripheral nerve & myelin

A human peripheral nerve is a heterogeneous fascicle assembly

Human · Block-face fluorescence
Cadaver tibial nerve; not index digital nerve

Compare fascicle number, size variation, connective tissue, vessels, and non-neural spaces.

Model differences and attribution

Four clean modeled fascicles underrepresent the irregular multi-fascicular composition of this particular nerve.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Kolluru et al., 2022 — Figure 4a; 3D-MUSE block face

© The Author(s) 2022Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

Source license

16 · Peripheral nerve & myelin

Myelinated fibers in human peripheral nerve

Human · UV-surface fluorescence
Cadaver tibial nerve

The source reveals varied ring diameters, shapes, and packing in a human nerve section.

Model differences and attribution

The model’s caliber and packing assumptions have not been fitted to these images or to an index-only nerve.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Kolluru et al., 2022 — Figure 3a-c; myelin-specific stain

Source license

17 · Peripheral nerve & myelin

Peripheral nerve microanatomy in three dimensions

Human · Optical volume rendering
Cadaver tibial nerve; intrafascicular volume

Compare longitudinal fiber organization within a tissue volume, rather than only isolated axons.

Model differences and attribution

The model contains a limited synthetic fiber sample and lacks the full connective-tissue texture of the source volume.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Kolluru et al., 2022 — Figure 4d; 3D-MUSE volume

Source license

18 · Peripheral nerve & myelin

Myelin rings and a nerve’s longitudinal appearance

Rat · UV-surface fluorescence
Sciatic nerve

The source includes a gap described as suggestive of a cleft or node, not definitively one or the other.

Model differences and attribution

V3 inserts explicit repeated nodal gaps. Their spacing and shape are not validated by this single optical image.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Kolluru et al., 2022 — Figure 2d-f; longitudinal view

Source license

19 · Peripheral nerve & myelin

Axonal caliber is not constant along a trajectory

Rat · Serial block-face EM reconstruction
Normal optic nerve; CNS analogue, not peripheral nerve

The traced axons vary visibly in thickness and cross-sectional profile along their length.

Model differences and attribution

This supports inspecting longitudinal shape variation, not transferring optic-nerve myelin organization directly to a digital nerve.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Giacci et al., 2018 — Figure 1a; reconstructed axons

Open-access Scientific Reports article; retain attribution.

Source license

20 · Peripheral nerve & myelin

One axon looks different in consecutive sections

Rat · Serial electron microscopy
Normal optic nerve; CNS analogue

Compare the changing profile of a highlighted axon across the serial image sequence.

Model differences and attribution

A single diameter and g-ratio cannot fully describe the longitudinally varying geometry shown here.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Giacci et al., 2018 — Figure 1b; serial sections

Open-access Scientific Reports article; retain attribution.

Source license

21 · Dorsal root ganglion

Human ganglion somata inside real tissue

Human · Immunohistology
Lumbar dorsal root ganglion; not cervical

The raw section shows large neuronal profiles embedded among many smaller structures and fibers.

Model differences and attribution

V3 isolates somata around a clean bundle. Real tissue packing and satellite-cell coverage are much less diagrammatic.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Sperry et al., 2020 — Figure 2, left; unsegmented image

The source retains its copyright and reuse terms; consult the original publication.

22 · Dorsal root ganglion

Human ganglion architecture at the tissue scale

Human · Immunohistology
Lumbar dorsal root ganglion

Compare the ganglion’s internal tissue compartments across sections, not just its external bulb.

Model differences and attribution

The model is a cellular inspection sample, not a calibrated whole-ganglion section or complete soma census.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Sperry et al., 2020 — Figure 1c; two NF200-stained section images

The source retains its copyright and reuse terms; consult the original publication.

23 · Dorsal root ganglion

Histology-derived three-dimensional ganglion compartments

Human · Histology-derived reconstruction
Lumbar L4 / L5 ganglia

The source resolves ganglion, ventral root, and enclosing tissue as distinct volumetric compartments.

Model differences and attribution

These are reconstructed tissue compartments, not segmented individual neurons. They should not be confused with a cellular connectome.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Sperry et al., 2020 — Figure 3a-b; reconstructed specimens

The source retains its copyright and reuse terms; consult the original publication.

24 · Dorsal root ganglion

Ganglion cellular packing in hematoxylin and eosin

Cat · Histology
Sacral S1 dorsal root ganglion

Compare nonuniform local cell packing and intervening tissue with the open model view.

Model differences and attribution

This is a feline sacral analogue. Neither its density nor its shape distribution is a direct human cervical calibration.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Ostrowski et al., 2017 — Figure 2, left; raw H&E section

The source retains its copyright and reuse terms; consult the original publication.

25 · Spinal cord, brainstem & thalamus

Cervical gray matter: neuronal distribution

Squirrel monkey · Immunohistology
Cervical spinal cord C5

Compare neuronal organization within dorsal and ventral gray matter across the whole section.

Model differences and attribution

The V3 section is normalized to a teaching composition; its cellular and whole-cord scales are not consistently calibrated.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Liao et al., 2015 — Figure 1A; NeuN

The source retains its copyright and reuse terms; consult the original publication.

26 · Spinal cord, brainstem & thalamus

Cervical gray matter in a Nissl-stained section

Squirrel monkey · Histology
Cervical spinal cord C5

The second stain provides a different view of cellular architecture in the same spinal region.

Model differences and attribution

Matching the butterfly-shaped outline alone does not establish correct laminar packing or motor-pool position.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Liao et al., 2015 — Figure 1B; Nissl

The source retains its copyright and reuse terms; consult the original publication.

27 · Spinal cord, brainstem & thalamus

The cuneate region in an adult human medulla

Human · Immunohistology
Adult caudal medulla; dorsal quadrant

Use this reference for regional boundaries around the cuneate nucleus and adjoining structures.

Model differences and attribution

The colored V3 relay cluster is not a registered reconstruction of these nuclei or of the actual tract crossing.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Del Fiacco et al., 2018 — Figure 3; TRPV1 and Klüver-Barrera

© 2018 by the authors.Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).

Source license

28 · Spinal cord, brainstem & thalamus

Human brainstem relay-cell profiles

Human · Histology
Adult human cuneate nucleus

Compare the real stained soma profiles and surrounding neuropil with modeled relay cells.

Model differences and attribution

A Nissl image does not reveal complete dendritic trees; it cannot validate the generator’s full arbor topology.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Del Fiacco et al., 2018 — Figure 4c; cuneate nucleus, Nissl

Source license

29 · Spinal cord, brainstem & thalamus

Measured VPL dendritic reconstructions

Mouse · Biocytin reconstruction
VPL and VPM thalamus; juvenile mice

VPL cells are shown above; VPM cells below provide a neighboring but different relay population. Compare branching without merging the two nuclei.

Model differences and attribution

V3 uses generated relay arbors. Neither mouse population is an imported human VPL reconstruction.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Studtmann et al., 2023 — Figure 4A; VPL above, VPM below for contrast

The source retains its copyright and reuse terms; consult the original publication.

30 · Cortex, connectomics & synapses

A cortical population viewed as individual reconstructed cells

Human · EM reconstruction
H01 temporal cortex; layer 2 interneuron gallery

Compare overlapping arbors and cellular diversity at the population level.

Model differences and attribution

V3 repeats ten light-microscopy source morphologies. It is not the dense, independently segmented H01 population.

Human light-microscopy tracing; generated membrane surface

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

H01 project gallery; Shapson-Coe et al., 2024 — H01 gallery: layer 2 interneurons

Harvard / Google Research H01 gallery and linked dataset. No blanket image relicensing is asserted.

31 · Cortex, connectomics & synapses

Cortical layers and cellular distribution

Human · EM-derived cell maps
H01 temporal cortex

The source gives a tissue-scale context for neuronal and non-neuronal distributions.

Model differences and attribution

V3 shows selected layer groups II, III, and V, not a complete six-layer cellular census or measured cortical slab.

Human light-microscopy tracing; generated membrane surface

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Shapson-Coe et al., 2024 — Figure 4; upper cellular / vascular maps

The source retains its copyright and reuse terms; consult the original publication.

32 · Cortex, connectomics & synapses

A pyramidal soma and its spiny dendrites

Human · EM reconstruction
H01 temporal cortex; different donor / cell

Compare soma-to-dendrite transitions, taper, irregular membrane shape, and visible spine-bearing branches.

Model differences and attribution

The left surface is generated around a light-microscopy trace; detailed spines are off and the EM synapse annotations are absent.

Human light-microscopy tracing; generated membrane surface

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Shapson-Coe et al., 2024 — Figure 5D; pyramidal neuron

The source retains its copyright and reuse terms; consult the original publication.

33 · Cortex, connectomics & synapses

Smooth-dendrite interneuron versus a traced model cell

Human · EM reconstruction
H01 temporal cortex; different cell and specimen

The source demonstrates that a realistic cell need not have the same spine pattern as a pyramidal neuron.

Model differences and attribution

This is a morphology comparison, not a claim that the left Allen specimen has the right H01 cell’s subtype or connectivity.

Human light-microscopy tracing; generated membrane surface

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Shapson-Coe et al., 2024 — Figure 5E; interneuron

The source retains its copyright and reuse terms; consult the original publication.

34 · Cortex, connectomics & synapses

A chandelier-cell reconstruction

Human · EM reconstruction
H01 temporal cortex; chandelier-cell gallery

Compare branching organization and the spatial reach of one reconstructed cell.

Model differences and attribution

The left source cell is not identified here as a chandelier cell; no matching axonal cartridge topology is claimed.

Human light-microscopy tracing; generated membrane surface

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

H01 project gallery; Shapson-Coe et al., 2024 — H01 gallery: chandelier cell

Harvard / Google Research H01 gallery and linked dataset. No blanket image relicensing is asserted.

35 · Cortex, connectomics & synapses

Raw electron microscopy behind a connectomics reconstruction

Human · EM + segmentation
H01 temporal cortical neuropil

The source links membrane-defined compartments to segmentation, rather than treating colors as biological boundaries.

Model differences and attribution

V3 is surface geometry without a corresponding raw EM volume; there is no voxel-to-membrane validation.

Human light-microscopy tracing; generated membrane surface

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Shapson-Coe et al., 2024 — Figure 2A-B; segmentation examples

The source retains its copyright and reuse terms; consult the original publication.

36 · Cortex, connectomics & synapses

Neuron surfaces annotated with synaptic inputs

Human · EM reconstruction + annotations
H01 temporal cortex

The points on the reference surface are annotations on reconstructed tissue, not decorative particles.

Model differences and attribution

V3 has no experimentally assigned synapse map. Adding dots to the model would not reproduce this evidence.

Human light-microscopy tracing; generated membrane surface

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

H01 project gallery; Shapson-Coe et al., 2024 — H01 gallery: excitatory / inhibitory synapses

Harvard / Google Research H01 gallery and linked dataset. No blanket image relicensing is asserted.

37 · Cortex, connectomics & synapses

Multiple axon-to-dendrite contacts in reconstructed tissue

Human · EM reconstruction
H01 temporal cortex; selected strong connection

This deliberately selected example shows multiple contacts between an axon and dendrite.

Model differences and attribution

The source is not a typical-contact-frequency prior. V3 lacks the measured partner identities and contact geometry.

Human light-microscopy tracing; generated membrane surface

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Shapson-Coe et al., 2024 — Figure 7A; selected eight-contact connection

The source retains its copyright and reuse terms; consult the original publication.

38 · Cortex, connectomics & synapses

A real thalamocortical synapse in thin section

Mouse · Transmission EM
VPM-to-barrel-cortex pathway; whisker system

Compare the nanoscale membrane apposition with what the model’s smooth neurite surfaces can actually represent.

Model differences and attribution

Synaptic clefts, postsynaptic densities, vesicles, and organelles are not resolved by the V3 source-cell surface.

Human light-microscopy tracing; generated membrane surface

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Rodriguez-Moreno et al., 2018 — Figure 3; synaptic contacts

© The Author 2017. Published by Oxford University Press.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [email protected]

Source license

39 · Cortex, connectomics & synapses

Bouton shape, vesicles, and mitochondria in three dimensions

Mouse · Serial TEM reconstruction
VPM thalamocortical boutons in barrel cortex

The source separates the bouton envelope from internal structures and postsynaptic contact regions.

Model differences and attribution

This is a detail target beyond current model resolution, not a scale-matched comparison of complete cells.

Human light-microscopy tracing; generated membrane surface

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Rodriguez-Moreno et al., 2018 — Figure 5B-F; reconstructed boutons

Source license

40 · Cortex, connectomics & synapses

Longitudinal axon segments and their bouton organization

Mouse · FIB-SEM reconstruction
Cortical thalamocortical axons; not peripheral nerve

Compare changes along a neurite instead of assuming one smooth, uniform shaft.

Model differences and attribution

The left is a peripheral-fiber model. CNS bouton morphology must not be added indiscriminately to peripheral nerve shafts.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Rodriguez-Moreno et al., 2018 — Figure 7A; segmented axonal excerpts

Source license

41 · Neuromuscular junction

Human motor endplates across lower-limb muscles

Human · Confocal microscopy
Lower-limb muscles; not index-finger muscle targets

Compare terminal branching, separate receptor domains, and irregular endplate shape.

Model differences and attribution

The V3 terminal is still bead-like and schematic. Human source geometry should replace, not merely decorate, that template.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Jones et al., 2017 — Figure 1A; human NMJ rows

42 · Neuromuscular junction

Human NMJs across adult decades

Human · Confocal microscopy
Peroneus longus; adult age groups

The source offers multiple actual human junctions rather than one canonical endplate shape.

Model differences and attribution

V3 contains one generated terminal example; it does not encode this between-sample variation or an age-dependent model.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Jones et al., 2017 — Figure 2A; adult decades

43 · Neuromuscular junction

Presynaptic protein organization below conventional resolution

Human · Super-resolution fluorescence
Lower-limb NMJ; presynaptic compartment

The reference resolves molecular labeling within a small presynaptic region.

Model differences and attribution

The left terminal surface has no molecular localization data. Its dots or swellings should not be interpreted as protein clusters.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Jones et al., 2017 — Figure 3a; human dSTORM panel

44 · Neuromuscular junction

Species differences matter at the motor endplate

Multiple species · Confocal microscopy
Human, mouse, cat, dog, sheep, and pig NMJs

Compare the different terminal and receptor patterns across species in the source montage.

Model differences and attribution

Do not copy the most familiar mouse endplate shape into a human model without labeling the substitution.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Boehm et al., 2020 — Figure 2; species comparison

© 2020 The Authors. Journal of Anatomy published by John Wiley & Sons Ltd on behalf of Anatomical SocietyThis is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Source license

45 · Proprioceptive endings

A spindle inside a real muscle cross-section

Sheep · Histology
Extraocular muscle spindle; not a finger-muscle specimen

The section shows intrafusal fibers, capsule, and surrounding extrafusal tissue together.

Model differences and attribution

V3 has a simplified longitudinal comparison specimen; its capsule and intrafusal architecture are not fitted to this section.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Rungaldier et al., 2009 — Figure 1; spindle section

The source retains its copyright and reuse terms; consult the original publication.

46 · Proprioceptive endings

Spindle sensory terminals among intrafusal fibers

Sheep · Confocal microscopy
Extraocular muscle spindle; equatorial region

Compare wrapping and branching around individual intrafusal fibers with the repeated model helices.

Model differences and attribution

The repeated geometry is too regular to stand in for individually traced endings and their associated supporting cells.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Rungaldier et al., 2009 — Figure 3C,E; sensory region

The source retains its copyright and reuse terms; consult the original publication.

47 · Proprioceptive endings

A spindle’s sensory interface under electron microscopy

Sheep · Transmission EM
Extraocular muscle spindle

The micrographs separate the capsule, sensory endings, motor ending, and muscle-fiber interfaces.

Model differences and attribution

The model does not contain the organelles, basal-lamina relationships, or synaptic ultrastructure visible here.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Rungaldier et al., 2009 — Figure 2; capsule and sensory / motor contacts

The source retains its copyright and reuse terms; consult the original publication.

48 · Proprioceptive endings

Golgi tendon-organ afferents in a whole-mount preparation

Sheep · Confocal microscopy
Extraocular muscle tendon organ

The source shows an afferent entering and branching within an actual tendon-organ preparation.

Model differences and attribution

V3 uses a generated arbor alongside generic collagen strands. This is a cross-muscle, cross-species morphology analogue.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Rungaldier et al., 2009 — Figure 5A; whole-mount GTO

The source retains its copyright and reuse terms; consult the original publication.

49 · Proprioceptive endings

Tendon-organ capsule and collagen relationships

Sheep · Histology
Extraocular muscle tendon organ

Compare the capsule and collagen-filled interior with the open longitudinal model.

Model differences and attribution

A realistic tendon organ needs the terminal embedded within its actual collagen architecture, not simply beside parallel strands.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Rungaldier et al., 2009 — Figure 4A; Azan-stained section

The source retains its copyright and reuse terms; consult the original publication.

50 · Proprioceptive endings

Tendon-organ endings between collagen fibrils

Sheep · Transmission EM
Extraocular muscle tendon organ

The source resolves terminals within collagen and the local supporting-cell relationship.

Model differences and attribution

The model has no fibril-scale packing, membrane contacts, or corresponding mechanical coupling.

Synthetic anatomical specimen; literature-informed model priors

Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.

Rungaldier et al., 2009 — Figure 4C-D; terminal / collagen contacts

The source retains its copyright and reuse terms; consult the original publication.

Sources and provenance

Original full figures and full-size supplied comparison plates are preserved. Gallery thumbnails are resized display copies. The comparison notes, crops, species, model basis and reference hashes remain in the comparison manifest; camera states and model-image provenance remain in the render provenance.

Download source bibliography

Chen et al., 2025 — Lamellar Schwann cells in the Pacinian corpuscle potentiate vibration perception · DOI: 10.1126/sciadv.adt5110
Jones et al., 2017 — Cellular and Molecular Anatomy of the Human Neuromuscular Junction · DOI: 10.1016/j.celrep.2017.11.008
Kim & Lee, 2020 — Re-evaluation of the distribution of Meissner’s corpuscles in human skin · DOI: 10.5115/acb.20.105
Shapson-Coe et al., 2024 — A petavoxel fragment of human cerebral cortex reconstructed at nanoscale resolution · DOI: 10.1126/science.adk4858
Liao et al., 2015 — Spinal cord neuron inputs to the cuneate nucleus that partially survive dorsal column lesions: a pathway that could contribute to recovery after spinal cord injury · DOI: 10.1002/cne.23783
Ostrowski et al., 2017 — Quantitative models of feline lumbosacral dorsal root ganglia neuronal cell density · DOI: 10.1016/j.jneumeth.2017.07.018
Studtmann et al., 2023 — Ventral posterolateral and ventral posteromedial thalamocortical neurons have distinct physiological properties · DOI: 10.1152/jn.00525.2022
Handler et al., 2023 — Three-dimensional reconstructions of mechanosensory end organs suggest a unifying mechanism underlying dynamic, light touch · DOI: 10.1016/j.neuron.2023.08.023
Rodriguez-Moreno et al., 2018 — Quantitative 3D Ultrastructure of Thalamocortical Synapses from the “Lemniscal” Ventral Posteromedial Nucleus in Mouse Barrel Cortex · DOI: 10.1093/cercor/bhx187
Del Fiacco et al., 2018 — TRPV1-Like Immunoreactivity in the Human Locus K, a Distinct Subregion of the Cuneate Nucleus · DOI: 10.3390/cells7070072
Van Acker et al., 2016 — Automated PGP9.5 immunofluorescence staining: a valuable tool in the assessment of small fiber neuropathy? · DOI: 10.1186/s13104-016-2085-4
Rungaldier et al., 2009 — Ultrastructural and molecular biologic comparison of classical proprioceptors and palisade endings in sheep extraocular muscles · DOI: 10.1167/iovs.09-3902
Hoffman et al., 2018 — MERKEL CELLS ACTIVATE SENSORY NEURAL PATHWAYS THROUGH ADRENERGIC SYNAPSES · DOI: 10.1016/j.neuron.2018.10.034
Kolluru et al., 2022 — Imaging peripheral nerve micro-anatomy with MUSE, 2D and 3D approaches · DOI: 10.1038/s41598-022-14166-1
Sperry et al., 2020 — Spatial models of cell distribution in human lumbar dorsal root ganglia · DOI: 10.1002/cne.24848
Boehm et al., 2020 — Comparative anatomy of the mammalian neuromuscular junction · DOI: 10.1111/joa.13260
Neubarth et al., 2020 — Meissner corpuscles and their spatially intermingled afferents underlie gentle touch perception · DOI: 10.1126/science.abb2751
Wu et al., 2024 — Discontinuity third harmonic generation microscopy for label-free imaging and quantification of intraepidermal nerve fibers · DOI: 10.1016/j.crmeth.2024.100735
Giacci et al., 2018 — Three dimensional electron microscopy reveals changing axonal and myelin morphology along normal and partially injured optic nerves · DOI: 10.1038/s41598-018-22361-2
H01 project gallery; Shapson-Coe et al., 2024 — H01 human cerebral cortex reconstruction gallery · DOI: 10.1126/science.adk4858