{ "version": "1.0", "model_version": "Finger Pathway Atlas v3", "created": "2026-10-14", "sources": [ { "id": "PMC12154225", "title": "Lamellar Schwann cells in the Pacinian corpuscle potentiate vibration perception", "authors": [ "Yuh-Tarng Chen", "Dominica de Thomas Wagner", "Alastair J Loutit", "Ali Nourizonoz", "Marina Ulanova", "Danai Graikou", "Man-Shan Chang", "Mary-Claude Croisier-Coeytaux", "Stéphanie Clerc-Rosset", "Jérôme Blanc", "Graham Knott", "Kuo-Sheng Lee", "Daniel Huber" ], "date": "2025 Jun 11", "doi": "10.1126/sciadv.adt5110", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12154225/", "rights_notice": "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.", "license_links": [ "https://creativecommons.org/licenses/by/4.0/" ], "short": "Chen et al., 2025", "selected_figures": [ "Figure 1; upper reconstruction panels", "Figure 2; upper contact-site panels", "Figure 3; lower EM junction panels" ] }, { "id": "PMC5723673", "title": "Cellular and Molecular Anatomy of the Human Neuromuscular Junction", "authors": [ "Ross A Jones", "Carl Harrison", "Samantha L Eaton", "Maica Llavero Hurtado", "Laura C Graham", "Leena Alkhammash", "Oladayo A Oladiran", "Andy Gale", "Douglas J Lamont", "Hamish Simpson", "Martin W Simmen", "Christian Soeller", "Thomas M Wishart", "Thomas H Gillingwater" ], "date": "2017 Nov 28", "doi": "10.1016/j.celrep.2017.11.008", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5723673/", "rights_notice": "© 2017 The Author(s)This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).", "license_links": [], "short": "Jones et al., 2017", "selected_figures": [ "Figure 1A; human NMJ rows", "Figure 2A; adult decades", "Figure 3a; human dSTORM panel" ] }, { "id": "PMC7527120", "title": "Re-evaluation of the distribution of Meissner’s corpuscles in human skin", "authors": [ "Sang Hyun Kim", "Young Ho Lee" ], "date": "2020 Sep 30", "doi": "10.5115/acb.20.105", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7527120/", "rights_notice": "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.", "license_links": [ "http://creativecommons.org/licenses/by-nc/4.0" ], "short": "Kim & Lee, 2020", "selected_figures": [ "Figure 1A; fingertip" ] }, { "id": "PMC11718559", "title": "A petavoxel fragment of human cerebral cortex reconstructed at nanoscale resolution", "authors": [ "Alexander Shapson-Coe", "Michał Januszewski", "Daniel R Berger", "Art Pope", "Yuelong Wu", "Tim Blakely", "Richard L Schalek", "Peter H Li", "Shuohong Wang", "Jeremy Maitin-Shepard", "Neha Karlupia", "Sven Dorkenwald", "Evelina Sjostedt", "Laramie Leavitt", "Dongil Lee", "Jakob Troidl", "Forrest Collman", "Luke Bailey", "Angerica Fitzmaurice", "Rohin Kar", "Benjamin Field", "Hank Wu", "Julian Wagner-Carena", "David Aley", "Joanna Lau", "Zudi Lin", "Donglai Wei", "Hanspeter Pfister", "Adi Peleg", "Viren Jain", "Jeff W Lichtman" ], "date": "2024 May 10", "doi": "10.1126/science.adk4858", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11718559/", "rights_notice": "", "license_links": [], "short": "Shapson-Coe et al., 2024", "selected_figures": [ "Figure 4; upper cellular / vascular maps", "Figure 5D; pyramidal neuron", "Figure 5E; interneuron", "Figure 2A-B; segmentation examples", "Figure 7A; selected multi-contact example" ] }, { "id": "PMC4575617", "title": "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", "authors": [ "Chia-Chi Liao", "Gabriella E DiCarlo", "Omar A Gharbawie", "Hui-Xin Qi", "Jon H Kaas" ], "date": "2015 Jun 2", "doi": "10.1002/cne.23783", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC4575617/", "rights_notice": "", "license_links": [], "short": "Liao et al., 2015", "selected_figures": [ "Figure 1A; NeuN", "Figure 1B; Nissl" ] }, { "id": "PMC5581694", "title": "Quantitative models of feline lumbosacral dorsal root ganglia neuronal cell density", "authors": [ "Anastasia K Ostrowski", "Zachariah J Sperry", "Grant Kulik", "Tim M Bruns" ], "date": "2017 Jul 21", "doi": "10.1016/j.jneumeth.2017.07.018", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5581694/", "rights_notice": "", "license_links": [], "short": "Ostrowski et al., 2017", "selected_figures": [ "Figure 2, left; raw H&E section" ] }, { "id": "PMC11068404", "title": "Ventral posterolateral and ventral posteromedial thalamocortical neurons have distinct physiological properties", "authors": [ "Carleigh Studtmann", "Marek Ladislav", "Mona Safari", "Rabeya Khondaker", "Yang Chen", "Grace A Vaughan", "Mackenzie A Topolski", "Eni Tomović", "Aleš Balík", "Sharon A Swanger" ], "date": "2023 Nov 8", "doi": "10.1152/jn.00525.2022", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11068404/", "rights_notice": "", "license_links": [], "short": "Studtmann et al., 2023", "selected_figures": [ "Figure 4A, top; VPL cells" ] }, { "id": "PMC10773061", "title": "Three-dimensional reconstructions of mechanosensory end organs suggest a unifying mechanism underlying dynamic, light touch", "authors": [ "Annie Handler", "Qiyu Zhang", "Song Pang", "Tri M Nguyen", "Michael Iskols", "Michael Nolan-Tamariz", "Stuart Cattel", "Rebecca Plumb", "Brianna Sanchez", "Karyl Ashjian", "Aria Shotland", "Bartianna Brown", "Madiha Kabeer", "Josef Turecek", "Michelle M DeLisle", "Genelle Rankin", "Wangchu Xiang", "Elisa C Pavarino", "Nusrat Africawala", "Celine Santiago", "Wei-Chung Allen Lee", "C Shan Xu", "David D Ginty" ], "date": "2023 Sep 18", "doi": "10.1016/j.neuron.2023.08.023", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10773061/", "rights_notice": "", "license_links": [], "short": "Handler et al., 2023", "selected_figures": [ "Figure 6A-B; afferents", "Figure 6C; lamellae and sections", "Figure 7A; whole-organ context", "Figure 7B; terminal region" ] }, { "id": "PMC6946031", "title": "Quantitative 3D Ultrastructure of Thalamocortical Synapses from the “Lemniscal” Ventral Posteromedial Nucleus in Mouse Barrel Cortex", "authors": [ "Javier Rodriguez-Moreno", "Astrid Rollenhagen", "Jaime Arlandis", "Andrea Santuy", "Angel Merchan-Pérez", "Javier DeFelipe", "Joachim H R Lübke", "Francisco Clasca" ], "date": "2017 Jul 28", "doi": "10.1093/cercor/bhx187", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC6946031/", "rights_notice": "© 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 journals.permissions@oup.com", "license_links": [ "http://creativecommons.org/licenses/by-nc/4.0/" ], "short": "Rodriguez-Moreno et al., 2018", "selected_figures": [ "Figure 3; synaptic contacts", "Figure 5B-F; reconstructed boutons", "Figure 7A; segmented axonal excerpts" ] }, { "id": "PMC6071077", "title": "TRPV1-Like Immunoreactivity in the Human Locus K, a Distinct Subregion of the Cuneate Nucleus", "authors": [ "Marina Del Fiacco", "Maria Pina Serra", "Marianna Boi", "Laura Poddighe", "Roberto Demontis", "Antonio Carai", "Marina Quartu" ], "date": "2018 Jul 8", "doi": "10.3390/cells7070072", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC6071077/", "rights_notice": "© 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/).", "license_links": [ "http://creativecommons.org/licenses/by/4.0/" ], "short": "Del Fiacco et al., 2018", "selected_figures": [ "Figure 3; TRPV1 and Klüver-Barrera", "Figure 4a,c,e; Nissl micrographs" ] }, { "id": "PMC4878004", "title": "Automated PGP9.5 immunofluorescence staining: a valuable tool in the assessment of small fiber neuropathy?", "authors": [ "Nathalie Van Acker", "Michael Ragé", "Ellen Sluydts", "Michiel W M Knaapen", "Martine De Bie", "Maarten Timmers", "Erik Fransen", "Carla Duymelinck", "Stefanie De Schepper", "Praveen Anand", "Theo Meert", "Léon Plaghki", "Patrick Cras" ], "date": "2016 May 23", "doi": "10.1186/s13104-016-2085-4", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC4878004/", "rights_notice": "© The Author(s). 2016https://creativecommons.org/licenses/by/4.0/\nOpen 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.", "license_links": [ "http://creativecommons.org/licenses/by/4.0/" ], "short": "Van Acker et al., 2016", "selected_figures": [ "Figure 3; PGP9.5 staining" ] }, { "id": "PMC4811329", "title": "Ultrastructural and molecular biologic comparison of classical proprioceptors and palisade endings in sheep extraocular muscles", "authors": [ "Stefanie RUNGALDIER", "Stefan HEILIGENBRUNNER", "Regina MAYER", "Christiane HANEFL-KRIVANEK", "Marietta LIPOWEC", "Johannes STREICHER", "Roland BLUMER" ], "date": "2009 Jun 24", "doi": "10.1167/iovs.09-3902", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC4811329/", "rights_notice": "", "license_links": [], "short": "Rungaldier et al., 2009", "selected_figures": [ "Figure 1; spindle section", "Figure 3C,E; sensory region", "Figure 2; capsule and sensory / motor contacts", "Figure 5A; whole-mount GTO", "Figure 4A; Azan-stained section", "Figure 4C-D; terminal / collagen contacts" ] }, { "id": "PMC6347413", "title": "MERKEL CELLS ACTIVATE SENSORY NEURAL PATHWAYS THROUGH ADRENERGIC SYNAPSES", "authors": [ "Benjamin U Hoffman", "Yoshichika Baba", "Theanne N Griffith", "Eugene V Mosharov", "Seung-Hyun Woo", "Daniel D Roybal", "Gerard Karsenty", "Ardem Patapoutian", "David Sulzer", "Ellen A Lumpkin" ], "date": "2018 Nov 8", "doi": "10.1016/j.neuron.2018.10.034", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC6347413/", "rights_notice": "", "license_links": [], "short": "Hoffman et al., 2018", "selected_figures": [ "Figure 1E; whole-mount touch dome" ] }, { "id": "PMC9205958", "title": "Imaging peripheral nerve micro-anatomy with MUSE, 2D and 3D approaches", "authors": [ "Chaitanya Kolluru", "Austin Todd", "Aniruddha R Upadhye", "Yehe Liu", "Mikhail Y Berezin", "Farzad Fereidouni", "Richard M Levenson", "Yanming Wang", "Andrew J Shoffstall", "Michael W Jenkins", "David L Wilson" ], "date": "2022 Jun 17", "doi": "10.1038/s41598-022-14166-1", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9205958/", "rights_notice": "© 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/.", "license_links": [ "https://creativecommons.org/licenses/by/4.0/" ], "short": "Kolluru et al., 2022", "selected_figures": [ "Figure 4a; 3D-MUSE block face", "Figure 3a-c; myelin-specific stain", "Figure 4d; 3D-MUSE volume", "Figure 2d-f; longitudinal view" ] }, { "id": "PMC7211131", "title": "Spatial models of cell distribution in human lumbar dorsal root ganglia", "authors": [ "Zachariah J Sperry", "Robert D Graham", "Nicholas Peck-Dimit", "Scott F Lempka", "Tim M Bruns" ], "date": "2020 Jan 6", "doi": "10.1002/cne.24848", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7211131/", "rights_notice": "", "license_links": [], "short": "Sperry et al., 2020", "selected_figures": [ "Figure 2, left; unsegmented image", "Figure 1c; histological sampling", "Figure 3a-b; reconstructed specimens" ] }, { "id": "PMC7542190", "title": "Comparative anatomy of the mammalian neuromuscular junction", "authors": [ "Ines Boehm", "Abrar Alhindi", "Ana S Leite", "Chandra Logie", "Alyssa Gibbs", "Olivia Murray", "Rizwan Farrukh", "Robert Pirie", "Christopher Proudfoot", "Richard Clutton", "Thomas M Wishart", "Ross A Jones", "Thomas H Gillingwater" ], "date": "2020 Jun 23", "doi": "10.1111/joa.13260", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7542190/", "rights_notice": "© 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.", "license_links": [ "http://creativecommons.org/licenses/by/4.0/" ], "short": "Boehm et al., 2020", "selected_figures": [ "Figure 2; species comparison" ] }, { "id": "PMC7354383", "title": "Meissner corpuscles and their spatially intermingled afferents underlie gentle touch perception", "authors": [ "Nicole L Neubarth", "Alan J Emanuel", "Yin Liu", "Mark W Springel", "Annie Handler", "Qiyu Zhang", "Brendan P Lehnert", "Chong Guo", "Lauren L Orefice", "Amira Abdelaziz", "Michelle M DeLisle", "Michael Iskols", "Julia Rhyins", "Soo J Kim", "Stuart J Cattel", "Wade Regehr", "Christopher D Harvey", "Jan Drugowitsch", "David D Ginty" ], "date": "2020 Jun 19", "doi": "10.1126/science.abb2751", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7354383/", "rights_notice": "", "license_links": [], "short": "Neubarth et al., 2020", "selected_figures": [ "Figure 6B; TrkB and Ret labeling", "Figure 6C; terminal close-ups" ] }, { "id": "PMC10985268", "title": "Discontinuity third harmonic generation microscopy for label-free imaging and quantification of intraepidermal nerve fibers", "authors": [ "Pei-Jhe Wu", "Hsiao-Chieh Tseng", "Chi-Chao Chao", "Yi-Hua Liao", "Chen-Tung Yen", "Wen-Ying Lin", "Sung-Tsang Hsieh", "Wei-Zen Sun", "Chi-Kuang Sun" ], "date": "2024 Mar 18", "doi": "10.1016/j.crmeth.2024.100735", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10985268/", "rights_notice": "© 2024 The Author(s)This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).", "license_links": [], "short": "Wu et al., 2024", "selected_figures": [ "Figure 2; epidermal nerve detail", "Figure 3; lower-right reconstruction panels" ] }, { "id": "GIACCI", "short": "Giacci et al., 2018", "title": "Three dimensional electron microscopy reveals changing axonal and myelin morphology along normal and partially injured optic nerves", "doi": "10.1038/s41598-018-22361-2", "url": "https://www.nature.com/articles/s41598-018-22361-2", "license_links": [ "https://creativecommons.org/licenses/by/4.0/" ], "rights_notice": "Open-access Scientific Reports article; retain attribution.", "selected_figures": [ "Figure 1a; reconstructed axons", "Figure 1b; serial sections" ] }, { "id": "H01G", "short": "H01 project gallery; Shapson-Coe et al., 2024", "title": "H01 human cerebral cortex reconstruction gallery", "doi": "10.1126/science.adk4858", "url": "https://h01-release.storage.googleapis.com/gallery.html", "license_links": [], "rights_notice": "Harvard / Google Research H01 gallery and linked dataset. No blanket image relicensing is asserted.", "selected_figures": [ "H01 gallery: layer 2 interneurons", "H01 gallery: chandelier cell", "H01 gallery: excitatory / inhibitory synapses" ] } ], "model_view_count": 27, "unique_reference_figures": 42, "primary_study_count": 19, "comparisons": [ { "number": 1, "group": "01 Skin & sensory endings", "title": "A Meissner corpuscle in human fingertip skin", "model": "meissner", "model_crop": null, "reference_source": "PMC7527120", "reference_file": "references/PMC7527120/F1.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9c21/7527120/498e5ffb1db7/ACB-53-325-f1.jpg", "reference_crop": [ 0, 0, 0.5, 1 ], "reference_sha256": "92f526505f5a1c0dd25d348b31e946cc021325e6590f4870887ae1a6964cad57", "species": "Human", "tissue": "Fingertip; cadaveric skin", "modality": "Histology", "panel": "Figure 1A; fingertip", "source_caption_title": "Fig. 1", "compare": "Compare the terminal-bearing corpuscle with its surrounding dermal papilla, not only the outer outline.", "gap": "The model is much more regular and isolated; surrounding cells and papillary attachment are simplified.", "reference_crop_pixels": [ 0, 0, 349, 226 ], "reference_native_size": [ 698, 226 ], "reference_selected_file": "references/selected/01.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/01_a_meissner_corpuscle_in_human_fingertip_skin.jpg", "model_asset": "m0", "reference_asset": "r1", "full_reference_asset": "f0", "full_figure_file": "reference_figures/PMC7527120_F1.jpg" }, { "number": 2, "group": "01 Skin & sensory endings", "title": "Meissner afferents: reconstructed terminal topology", "model": "meissner_core", "model_crop": null, "reference_source": "PMC10773061", "reference_file": "references/PMC10773061/F6.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5007/10773061/a2c79d00f19b/nihms-1949993-f0007.jpg", "reference_crop": [ 0, 0, 1, 0.37 ], "reference_sha256": "cd0ccd94960350d711dfa1f089b43ace795feb1d3f4ea87b40c9f2d175ea9faa", "species": "Mouse", "tissue": "Glabrous skin; Meissner corpuscle", "modality": "EM reconstruction", "panel": "Figure 6A-B; traced afferents with orientation drawings", "source_caption_title": "Figure 6", "compare": "The reference separates two traced afferents and shows a highly folded terminal contour.", "gap": "The modeled repeating loops are a visual placeholder, not the reconstructed arbor shown at right.", "reference_crop_pixels": [ 0, 0, 1500, 669 ], "reference_native_size": [ 1500, 1808 ], "reference_selected_file": "references/selected/02.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/02_meissner_afferents_reconstructed_terminal_topology.jpg", "model_asset": "m1", "reference_asset": "r2", "full_reference_asset": "f1", "full_figure_file": "reference_figures/PMC10773061_F6.jpg" }, { "number": 3, "group": "01 Skin & sensory endings", "title": "Meissner supporting lamellae and axon relationships", "model": "meissner", "model_crop": null, "reference_source": "PMC10773061", "reference_file": "references/PMC10773061/F6.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5007/10773061/a2c79d00f19b/nihms-1949993-f0007.jpg", "reference_crop": [ 0, 0.372, 1, 0.604 ], "reference_sha256": "cd0ccd94960350d711dfa1f089b43ace795feb1d3f4ea87b40c9f2d175ea9faa", "species": "Mouse", "tissue": "Glabrous skin; Meissner corpuscle", "modality": "EM reconstruction", "panel": "Figure 6C; supporting cells and colored EM sections", "source_caption_title": "Figure 6", "compare": "Compare the relative positions of axon and supporting cells across the reconstructed corpuscle.", "gap": "The model uses repeated flattened shells; real lamellar cells need individual boundaries and nonuniform contacts.", "reference_crop_pixels": [ 0, 673, 1500, 1092 ], "reference_native_size": [ 1500, 1808 ], "reference_selected_file": "references/selected/03.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/03_meissner_supporting_lamellae_and_axon_relationships.jpg", "model_asset": "m0", "reference_asset": "r3", "full_reference_asset": "f1", "full_figure_file": "reference_figures/PMC10773061_F6.jpg" }, { "number": 4, "group": "01 Skin & sensory endings", "title": "Meissner corpuscles in an electron-microscope section", "model": "meissner", "model_crop": null, "reference_source": "PMC7354383", "reference_file": "references/PMC7354383/F6.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7389/7354383/0016cb17c8b0/nihms-1606072-f0006.jpg", "reference_crop": [ 0.32, 0, 1, 0.58 ], "reference_sha256": "9008ffc23ff5d2d387b562473a7a5f2e7ef1fb15f60dab9eda70774c3d186471", "species": "Mouse", "tissue": "Digit-tip Meissner corpuscles; genetically labeled endings", "modality": "Electron microscopy", "panel": "Figure 6B; TrkB and Ret labeling", "source_caption_title": "Figure 6", "compare": "The two source sections expose irregular axonal profiles among closely packed lamellae.", "gap": "This is a section-versus-surface comparison. A 3D outer shell cannot substitute for the internal section pattern.", "reference_crop_pixels": [ 614, 0, 1920, 936 ], "reference_native_size": [ 1920, 1613 ], "reference_selected_file": "references/selected/04.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/04_meissner_corpuscles_in_an_electron_microscope_section.jpg", "model_asset": "m0", "reference_asset": "r4", "full_reference_asset": "f2", "full_figure_file": "reference_figures/PMC7354383_F6.jpg" }, { "number": 5, "group": "01 Skin & sensory endings", "title": "Meissner terminal ultrastructure", "model": "meissner_core", "model_crop": null, "reference_source": "PMC7354383", "reference_file": "references/PMC7354383/F6.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7389/7354383/0016cb17c8b0/nihms-1606072-f0006.jpg", "reference_crop": [ 0, 0.588, 0.705, 0.99 ], "reference_sha256": "9008ffc23ff5d2d387b562473a7a5f2e7ef1fb15f60dab9eda70774c3d186471", "species": "Mouse", "tissue": "Digit-tip Meissner corpuscles", "modality": "Electron microscopy", "panel": "Figure 6C; terminal close-ups", "source_caption_title": "Figure 6", "compare": "Inspect the gap between a smooth modeled membrane and organelle-containing, closely apposed tissue.", "gap": "Mitochondria, membrane junctions, and the source-specific supporting-cell arrangement are not modeled.", "reference_crop_pixels": [ 0, 948, 1354, 1597 ], "reference_native_size": [ 1920, 1613 ], "reference_selected_file": "references/selected/05.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/05_meissner_terminal_ultrastructure.jpg", "model_asset": "m1", "reference_asset": "r5", "full_reference_asset": "f2", "full_figure_file": "reference_figures/PMC7354383_F6.jpg" }, { "number": 6, "group": "01 Skin & sensory endings", "title": "Merkel complexes in an intact touch dome", "model": "merkel", "model_crop": null, "reference_source": "PMC6347413", "reference_file": "references/PMC6347413/F1.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/db4e/6347413/3b8ceea924c7/nihms-1510833-f0001.jpg", "reference_crop": [ 0, 0.888, 0.498, 1 ], "reference_sha256": "bc91b05a25506b5e1fff3fd87453859099c18daac0db6410a54065984be489d9", "species": "Mouse", "tissue": "Hairy-skin touch dome; not a glabrous fingertip", "modality": "Immunofluorescence", "panel": "Figure 1E; whole-mount touch dome", "source_caption_title": "Figure 1", "compare": "Compare a branching afferent contacting several Merkel-cell profiles with the labeled cellular cluster.", "gap": "The tissue site differs. The model lacks the measured cluster geometry and surrounding keratinocyte boundaries.", "reference_crop_pixels": [ 0, 932, 389, 1050 ], "reference_native_size": [ 781, 1050 ], "reference_selected_file": "references/selected/06.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/06_merkel_complexes_in_an_intact_touch_dome.jpg", "model_asset": "m2", "reference_asset": "r6", "full_reference_asset": "f3", "full_figure_file": "reference_figures/PMC6347413_F1.jpg" }, { "number": 7, "group": "01 Skin & sensory endings", "title": "The Pacinian organ and its reconstructed sensory ending", "model": "pacinian", "model_crop": null, "reference_source": "PMC10773061", "reference_file": "references/PMC10773061/F7.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5007/10773061/fba8790592ea/nihms-1949993-f0008.jpg", "reference_crop": [ 0, 0, 1, 0.28 ], "reference_sha256": "5dd6f39df9579ccf7a3718b8f64860bd7054b9741b0ef454a01051c9f88d6913", "species": "Mouse", "tissue": "Pacinian corpuscle near fibula; not a human finger", "modality": "Tomography + EM reconstruction", "panel": "Figure 7A; whole-organ context", "source_caption_title": "Figure 7", "compare": "Compare the organ envelope and long central ending while keeping the two imaging modalities distinct.", "gap": "The model shows an idealized capsule. It does not reproduce the traced terminal protrusions or exact inner-core anatomy.", "reference_crop_pixels": [ 0, 0, 1500, 553 ], "reference_native_size": [ 1500, 1974 ], "reference_selected_file": "references/selected/07.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/07_the_pacinian_organ_and_its_reconstructed_sensory_ending.jpg", "model_asset": "m3", "reference_asset": "r7", "full_reference_asset": "f4", "full_figure_file": "reference_figures/PMC10773061_F7.jpg" }, { "number": 8, "group": "01 Skin & sensory endings", "title": "Pacinian terminal protrusions and inner-core contact", "model": "pacinian_core", "model_crop": null, "reference_source": "PMC10773061", "reference_file": "references/PMC10773061/F7.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5007/10773061/fba8790592ea/nihms-1949993-f0008.jpg", "reference_crop": [ 0, 0.28, 1, 0.65 ], "reference_sha256": "5dd6f39df9579ccf7a3718b8f64860bd7054b9741b0ef454a01051c9f88d6913", "species": "Mouse", "tissue": "Fibular Pacinian corpuscle", "modality": "EM reconstruction", "panel": "Figure 7B; terminal region", "source_caption_title": "Figure 7", "compare": "The reference resolves terminal surface projections that disappear in a smooth capsule-based representation.", "gap": "The side-on V3 cutaway still obscures much of the central ending; its inner-core microgeometry needs rebuilding.", "reference_crop_pixels": [ 0, 553, 1500, 1283 ], "reference_native_size": [ 1500, 1974 ], "reference_selected_file": "references/selected/08.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/08_pacinian_terminal_protrusions_and_inner_core_contact.jpg", "model_asset": "m4", "reference_asset": "r8", "full_reference_asset": "f4", "full_figure_file": "reference_figures/PMC10773061_F7.jpg" }, { "number": 9, "group": "01 Skin & sensory endings", "title": "Pacinian lamellar Schwann cells are complex individual cells", "model": "pacinian", "model_crop": null, "reference_source": "PMC12154225", "reference_file": "references/PMC12154225/F1.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8962/12154225/80044e066d93/sciadv.adt5110-f1.jpg", "reference_crop": [ 0, 0.26, 1, 0.584 ], "reference_sha256": "5130ad91d5007a257ffe075c3dfebb75c876a51c0168b6928b39db091dfe01c5", "species": "Mouse", "tissue": "Fibular Pacinian inner core", "modality": "EM reconstruction", "panel": "Figure 1B-C; individual lamellar Schwann cells and axon", "source_caption_title": "Fig. 1.", "compare": "Compare repeated modeled lamellae with individually reconstructed, interleaved supporting cells.", "gap": "One nested shell per layer is not equivalent to one real Schwann cell; topology and contacts remain missing.", "reference_crop_pixels": [ 0, 259, 775, 583 ], "reference_native_size": [ 775, 998 ], "reference_selected_file": "references/selected/09.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/09_pacinian_lamellar_schwann_cells_are_complex_individual_cells.jpg", "model_asset": "m3", "reference_asset": "r9", "full_reference_asset": "f5", "full_figure_file": "reference_figures/PMC12154225_F1.jpg" }, { "number": 10, "group": "01 Skin & sensory endings", "title": "Axon-to-lamellar-cell contact sites", "model": "pacinian_core", "model_crop": null, "reference_source": "PMC12154225", "reference_file": "references/PMC12154225/F2.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8962/12154225/82b495ca568a/sciadv.adt5110-f2.jpg", "reference_crop": [ 0.211, 0, 0.733, 0.229 ], "reference_sha256": "139a53ade2f29713a8adc8b8dc768de2ef333313ea07003684606c66f9de16d1", "species": "Mouse", "tissue": "Pacinian inner core", "modality": "EM reconstruction", "panel": "Figure 2B-C; axon body and protrusions", "source_caption_title": "Fig. 2.", "compare": "The source explicitly locates contacts on the axon body and its protrusions.", "gap": "No measured cell-to-cell contact map is encoded in the V3 Pacinian specimen.", "reference_crop_pixels": [ 168, 0, 583, 197 ], "reference_native_size": [ 796, 862 ], "reference_selected_file": "references/selected/10.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/10_axon_to_lamellar_cell_contact_sites.jpg", "model_asset": "m4", "reference_asset": "r10", "full_reference_asset": "f6", "full_figure_file": "reference_figures/PMC12154225_F2.jpg" }, { "number": 11, "group": "01 Skin & sensory endings", "title": "Pacinian support-cell junctions at nanometer scale", "model": "pacinian", "model_crop": null, "reference_source": "PMC12154225", "reference_file": "references/PMC12154225/F3.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8962/12154225/7b1a436e6271/sciadv.adt5110-f3.jpg", "reference_crop": [ 0, 0.37, 1, 1 ], "reference_sha256": "a4869386aee419c2844a970dc28a94522b1d8e0354387fced91ba40ac5cb4574", "species": "Mouse", "tissue": "Pacinian lamellar cells", "modality": "Electron microscopy", "panel": "Figure 3; lower EM junction panels", "source_caption_title": "Fig. 3.", "compare": "These micrographs show the level of membrane detail absent from an organ-scale surface model.", "gap": "This is an ultrastructure target, not a claim that such junctions are presently visible or simulated.", "reference_crop_pixels": [ 0, 356, 750, 961 ], "reference_native_size": [ 750, 961 ], "reference_selected_file": "references/selected/11.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/11_pacinian_support_cell_junctions_at_nanometer_scale.jpg", "model_asset": "m3", "reference_asset": "r11", "full_reference_asset": "f7", "full_figure_file": "reference_figures/PMC12154225_F3.jpg" }, { "number": 12, "group": "01 Skin & sensory endings", "title": "Free nerve endings in healthy human skin", "model": "free", "model_crop": null, "reference_source": "PMC4878004", "reference_file": "references/PMC4878004/Fig3.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f1a6/4878004/31f41084b9e9/13104_2016_2085_Fig3_HTML.jpg", "reference_crop": [ 0, 0, 1, 1 ], "reference_sha256": "6956a6b3ca60cab7090cc6c8c6c120ee9b23245b59988c3606361880c157a8c2", "species": "Human", "tissue": "Healthy volunteer skin biopsy; lower-limb site", "modality": "Immunofluorescence", "panel": "Figure 3; PGP9.5 staining", "source_caption_title": "Fig. 3", "compare": "Compare irregular fine branches crossing skin layers with the model’s unencapsulated arbor.", "gap": "The model does not reproduce the actual epidermal trajectory, varicosities, or fiber density of this biopsy.", "reference_crop_pixels": [ 0, 0, 711, 626 ], "reference_native_size": [ 711, 626 ], "reference_selected_file": "references/selected/12.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/12_free_nerve_endings_in_healthy_human_skin.jpg", "model_asset": "m5", "reference_asset": "r12", "full_reference_asset": "f8", "full_figure_file": "reference_figures/PMC4878004_Fig3.jpg" }, { "number": 13, "group": "01 Skin & sensory endings", "title": "Varicose epidermal fibers in human sole skin", "model": "free", "model_crop": null, "reference_source": "PMC10985268", "reference_file": "references/PMC10985268/fig2.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a4e/10985268/bda88a95eeea/gr2.jpg", "reference_crop": [ 0, 0.22, 1, 0.79 ], "reference_sha256": "4dfef8ee1da27c1766bdff41d6766311a09f40de42c31289d3b9be76b059a02a", "species": "Human", "tissue": "Sole skin; not fingertip skin", "modality": "Immunohistology", "panel": "Figure 2B-G; epidermal fibers and varicosities", "source_caption_title": "Figure 2", "compare": "The source makes the bead-like changes along very fine epidermal fibers visible.", "gap": "V3 has comparatively smooth fine branches. Sole and fingertip specimens should not share an unqualified density prior.", "reference_crop_pixels": [ 0, 198, 748, 711 ], "reference_native_size": [ 748, 900 ], "reference_selected_file": "references/selected/13.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/13_varicose_epidermal_fibers_in_human_sole_skin.jpg", "model_asset": "m5", "reference_asset": "r13", "full_reference_asset": "f9", "full_figure_file": "reference_figures/PMC10985268_fig2.jpg" }, { "number": 14, "group": "01 Skin & sensory endings", "title": "Human epidermal fibers reconstructed from label-free signals", "model": "free", "model_crop": null, "reference_source": "PMC10985268", "reference_file": "references/PMC10985268/fig3.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5a4e/10985268/59c9fbbfa8d5/gr3.jpg", "reference_crop": [ 0.591, 0.33, 1, 0.77 ], "reference_sha256": "93fb3ea83e2ae6c583af7e9155c9bf00090cd03b6c2639d6749c7c2965737f6d", "species": "Human", "tissue": "Ex vivo sole skin", "modality": "Optical reconstruction", "panel": "Figure 3N-Q; projection and 3D views", "source_caption_title": "Figure 3", "compare": "Compare the 3D course of signal-defined fibers with the model’s branching tree.", "gap": "This optical reconstruction is not EM membrane segmentation; neither panel is a complete epidermal connectome.", "reference_crop_pixels": [ 421, 307, 712, 716 ], "reference_native_size": [ 712, 930 ], "reference_selected_file": "references/selected/14.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/14_human_epidermal_fibers_reconstructed_from_label_free_signals.jpg", "model_asset": "m5", "reference_asset": "r14", "full_reference_asset": "f10", "full_figure_file": "reference_figures/PMC10985268_fig3.jpg" }, { "number": 15, "group": "02 Peripheral nerve & myelin", "title": "A human peripheral nerve is a heterogeneous fascicle assembly", "model": "nerve_cross", "model_crop": null, "reference_source": "PMC9205958", "reference_file": "references/PMC9205958/Fig4.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6986/9205958/2e9e664a860a/41598_2022_14166_Fig4_HTML.jpg", "reference_crop": [ 0, 0, 0.72, 0.5 ], "reference_sha256": "09007257fee3f654973fea8aa4e373669a3831882e6932de1e6a43969044f53e", "species": "Human", "tissue": "Cadaver tibial nerve; not index digital nerve", "modality": "Block-face fluorescence", "panel": "Figure 4a; 3D-MUSE block face", "source_caption_title": "Figure 4", "compare": "Compare fascicle number, size variation, connective tissue, vessels, and non-neural spaces.", "gap": "Four clean modeled fascicles underrepresent the irregular multi-fascicular composition of this particular nerve.", "reference_crop_pixels": [ 0, 0, 539, 328 ], "reference_native_size": [ 749, 655 ], "reference_selected_file": "references/selected/15.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/15_a_human_peripheral_nerve_is_a_heterogeneous_fascicle_assembly.jpg", "model_asset": "m6", "reference_asset": "r15", "full_reference_asset": "f11", "full_figure_file": "reference_figures/PMC9205958_Fig4.jpg" }, { "number": 16, "group": "02 Peripheral nerve & myelin", "title": "Myelinated fibers in human peripheral nerve", "model": "nerve_cut_detail", "model_crop": null, "reference_source": "PMC9205958", "reference_file": "references/PMC9205958/Fig3.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6986/9205958/75f1ea045448/41598_2022_14166_Fig3_HTML.jpg", "reference_crop": [ 0, 0, 1, 1 ], "reference_sha256": "5baf1b16b34b0d676c8d369d2bd6468e60466318b11b1da3443791621920d05c", "species": "Human", "tissue": "Cadaver tibial nerve", "modality": "UV-surface fluorescence", "panel": "Figure 3a-c; myelin-specific stain", "source_caption_title": "Figure 3", "compare": "The source reveals varied ring diameters, shapes, and packing in a human nerve section.", "gap": "The model’s caliber and packing assumptions have not been fitted to these images or to an index-only nerve.", "reference_crop_pixels": [ 0, 0, 749, 419 ], "reference_native_size": [ 749, 419 ], "reference_selected_file": "references/selected/16.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/16_myelinated_fibers_in_human_peripheral_nerve.jpg", "model_asset": "m7", "reference_asset": "r16", "full_reference_asset": "f12", "full_figure_file": "reference_figures/PMC9205958_Fig3.jpg" }, { "number": 17, "group": "02 Peripheral nerve & myelin", "title": "Peripheral nerve microanatomy in three dimensions", "model": "nerve", "model_crop": null, "reference_source": "PMC9205958", "reference_file": "references/PMC9205958/Fig4.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6986/9205958/2e9e664a860a/41598_2022_14166_Fig4_HTML.jpg", "reference_crop": [ 0, 0.5, 0.51, 1 ], "reference_sha256": "09007257fee3f654973fea8aa4e373669a3831882e6932de1e6a43969044f53e", "species": "Human", "tissue": "Cadaver tibial nerve; intrafascicular volume", "modality": "Optical volume rendering", "panel": "Figure 4d; 3D-MUSE volume", "source_caption_title": "Figure 4", "compare": "Compare longitudinal fiber organization within a tissue volume, rather than only isolated axons.", "gap": "The model contains a limited synthetic fiber sample and lacks the full connective-tissue texture of the source volume.", "reference_crop_pixels": [ 0, 328, 382, 655 ], "reference_native_size": [ 749, 655 ], "reference_selected_file": "references/selected/17.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/17_peripheral_nerve_microanatomy_in_three_dimensions.jpg", "model_asset": "m8", "reference_asset": "r17", "full_reference_asset": "f11", "full_figure_file": "reference_figures/PMC9205958_Fig4.jpg" }, { "number": 18, "group": "02 Peripheral nerve & myelin", "title": "Myelin rings and a nerve’s longitudinal appearance", "model": "nerve_node_detail", "model_crop": null, "reference_source": "PMC9205958", "reference_file": "references/PMC9205958/Fig2.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6986/9205958/484b7f376c1d/41598_2022_14166_Fig2_HTML.jpg", "reference_crop": [ 0.48, 0, 1, 1 ], "reference_sha256": "7087231c47d6fb58f8434120a670177e06f4e0f616641f131ccf11af28d1238b", "species": "Rat", "tissue": "Sciatic nerve", "modality": "UV-surface fluorescence", "panel": "Figure 2d-f; longitudinal view", "source_caption_title": "Figure 2", "compare": "The source includes a gap described as suggestive of a cleft or node, not definitively one or the other.", "gap": "V3 inserts explicit repeated nodal gaps. Their spacing and shape are not validated by this single optical image.", "reference_crop_pixels": [ 321, 0, 668, 207 ], "reference_native_size": [ 668, 207 ], "reference_selected_file": "references/selected/18.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/18_myelin_rings_and_a_nerve_s_longitudinal_appearance.jpg", "model_asset": "m9", "reference_asset": "r18", "full_reference_asset": "f13", "full_figure_file": "reference_figures/PMC9205958_Fig2.jpg" }, { "number": 19, "group": "02 Peripheral nerve & myelin", "title": "Axonal caliber is not constant along a trajectory", "model": "nerve_fibers", "model_crop": null, "reference_source": "GIACCI", "reference_file": "references/giacci_f1.jpg", "reference_image_url": "https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41598-018-22361-2/MediaObjects/41598_2018_22361_Fig1_HTML.jpg", "reference_crop": [ 0, 0, 1, 0.617 ], "reference_sha256": "236c345a876981eee26dfb6a110bbcebf3b7e342cfcff31397eee3bafacaf180", "species": "Rat", "tissue": "Normal optic nerve; CNS analogue, not peripheral nerve", "modality": "Serial block-face EM reconstruction", "panel": "Figure 1a; reconstructed axons", "source_caption_title": "Figure 1a; reconstructed axons", "compare": "The traced axons vary visibly in thickness and cross-sectional profile along their length.", "gap": "This supports inspecting longitudinal shape variation, not transferring optic-nerve myelin organization directly to a digital nerve.", "reference_crop_pixels": [ 0, 0, 1500, 1042 ], "reference_native_size": [ 1500, 1689 ], "reference_selected_file": "references/selected/19.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/19_axonal_caliber_is_not_constant_along_a_trajectory.jpg", "model_asset": "m10", "reference_asset": "r19", "full_reference_asset": "f14", "full_figure_file": "reference_figures/GIACCI_giacci_f1.jpg" }, { "number": 20, "group": "02 Peripheral nerve & myelin", "title": "One axon looks different in consecutive sections", "model": "nerve_cut_detail", "model_crop": null, "reference_source": "GIACCI", "reference_file": "references/giacci_f1.jpg", "reference_image_url": "https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41598-018-22361-2/MediaObjects/41598_2018_22361_Fig1_HTML.jpg", "reference_crop": [ 0, 0.618, 1, 1 ], "reference_sha256": "236c345a876981eee26dfb6a110bbcebf3b7e342cfcff31397eee3bafacaf180", "species": "Rat", "tissue": "Normal optic nerve; CNS analogue", "modality": "Serial electron microscopy", "panel": "Figure 1b; serial sections", "source_caption_title": "Figure 1b; serial sections", "compare": "Compare the changing profile of a highlighted axon across the serial image sequence.", "gap": "A single diameter and g-ratio cannot fully describe the longitudinally varying geometry shown here.", "reference_crop_pixels": [ 0, 1044, 1500, 1689 ], "reference_native_size": [ 1500, 1689 ], "reference_selected_file": "references/selected/20.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/20_one_axon_looks_different_in_consecutive_sections.jpg", "model_asset": "m7", "reference_asset": "r20", "full_reference_asset": "f14", "full_figure_file": "reference_figures/GIACCI_giacci_f1.jpg" }, { "number": 21, "group": "03 Dorsal root ganglion", "title": "Human ganglion somata inside real tissue", "model": "drg_close", "model_crop": null, "reference_source": "PMC7211131", "reference_file": "references/PMC7211131/F2.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ac4b/7211131/bbd7735aee7e/nihms-1547059-f0003.jpg", "reference_crop": [ 0, 0, 0.334, 1 ], "reference_sha256": "326339a268f8136e2c0f01157dd348019aec18972815d9b723228479fed1650d", "species": "Human", "tissue": "Lumbar dorsal root ganglion; not cervical", "modality": "Immunohistology", "panel": "Figure 2, left; unsegmented image", "source_caption_title": "Figure 2", "compare": "The raw section shows large neuronal profiles embedded among many smaller structures and fibers.", "gap": "V3 isolates somata around a clean bundle. Real tissue packing and satellite-cell coverage are much less diagrammatic.", "reference_crop_pixels": [ 0, 0, 267, 300 ], "reference_native_size": [ 800, 300 ], "reference_selected_file": "references/selected/21.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/21_human_ganglion_somata_inside_real_tissue.jpg", "model_asset": "m11", "reference_asset": "r21", "full_reference_asset": "f15", "full_figure_file": "reference_figures/PMC7211131_F2.jpg" }, { "number": 22, "group": "03 Dorsal root ganglion", "title": "Human ganglion architecture at the tissue scale", "model": "drg", "model_crop": null, "reference_source": "PMC7211131", "reference_file": "references/PMC7211131/F1.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ac4b/7211131/bbb9d1749599/nihms-1547059-f0002.jpg", "reference_crop": [ 0.69, 0.285, 1, 0.538 ], "reference_sha256": "59e23323224a42ca9f21172f5f45f61c6b6fd1ef164f81e728bf6b182c56fba2", "species": "Human", "tissue": "Lumbar dorsal root ganglion", "modality": "Immunohistology", "panel": "Figure 1c; two NF200-stained section images", "source_caption_title": "Figure 1", "compare": "Compare the ganglion’s internal tissue compartments across sections, not just its external bulb.", "gap": "The model is a cellular inspection sample, not a calibrated whole-ganglion section or complete soma census.", "reference_crop_pixels": [ 518, 119, 750, 224 ], "reference_native_size": [ 750, 417 ], "reference_selected_file": "references/selected/22.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/22_human_ganglion_architecture_at_the_tissue_scale.jpg", "model_asset": "m12", "reference_asset": "r22", "full_reference_asset": "f16", "full_figure_file": "reference_figures/PMC7211131_F1.jpg" }, { "number": 23, "group": "03 Dorsal root ganglion", "title": "Histology-derived three-dimensional ganglion compartments", "model": "drg", "model_crop": null, "reference_source": "PMC7211131", "reference_file": "references/PMC7211131/F3.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ac4b/7211131/be34edf17288/nihms-1547059-f0004.jpg", "reference_crop": [ 0, 0, 1, 0.49 ], "reference_sha256": "9100094d1e5942d5a4b5d02ca21253b074d1866cb52ca156738b89ad31971d37", "species": "Human", "tissue": "Lumbar L4 / L5 ganglia", "modality": "Histology-derived reconstruction", "panel": "Figure 3a-b; reconstructed specimens", "source_caption_title": "Figure 3", "compare": "The source resolves ganglion, ventral root, and enclosing tissue as distinct volumetric compartments.", "gap": "These are reconstructed tissue compartments, not segmented individual neurons. They should not be confused with a cellular connectome.", "reference_crop_pixels": [ 0, 0, 800, 318 ], "reference_native_size": [ 800, 648 ], "reference_selected_file": "references/selected/23.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/23_histology_derived_three_dimensional_ganglion_compartments.jpg", "model_asset": "m12", "reference_asset": "r23", "full_reference_asset": "f17", "full_figure_file": "reference_figures/PMC7211131_F3.jpg" }, { "number": 24, "group": "03 Dorsal root ganglion", "title": "Ganglion cellular packing in hematoxylin and eosin", "model": "drg_close", "model_crop": null, "reference_source": "PMC5581694", "reference_file": "references/PMC5581694/F2.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d068/5581694/0a107b28dc16/nihms898140f2.jpg", "reference_crop": [ 0, 0, 0.5, 1 ], "reference_sha256": "1bd9f9b45ca163b40ab707ab4acdba9ddff7e46b6d75217cb049b6a806a8f8e0", "species": "Cat", "tissue": "Sacral S1 dorsal root ganglion", "modality": "Histology", "panel": "Figure 2, left; raw H&E section", "source_caption_title": "Figure 2", "compare": "Compare nonuniform local cell packing and intervening tissue with the open model view.", "gap": "This is a feline sacral analogue. Neither its density nor its shape distribution is a direct human cervical calibration.", "reference_crop_pixels": [ 0, 0, 256, 681 ], "reference_native_size": [ 511, 681 ], "reference_selected_file": "references/selected/24.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/24_ganglion_cellular_packing_in_hematoxylin_and_eosin.jpg", "model_asset": "m11", "reference_asset": "r24", "full_reference_asset": "f18", "full_figure_file": "reference_figures/PMC5581694_F2.jpg" }, { "number": 25, "group": "04 Spinal cord, brainstem & thalamus", "title": "Cervical gray matter: neuronal distribution", "model": "spinal", "model_crop": null, "reference_source": "PMC4575617", "reference_file": "references/PMC4575617/F1.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/925a/4575617/f8d71f50313a/nihms677959f1.jpg", "reference_crop": [ 0, 0, 1, 0.484 ], "reference_sha256": "e9b63a5d029ad5a742a803a69c76b78d690dc6f6b407670d162709e69d2f7eca", "species": "Squirrel monkey", "tissue": "Cervical spinal cord C5", "modality": "Immunohistology", "panel": "Figure 1A; NeuN", "source_caption_title": "Figure 1", "compare": "Compare neuronal organization within dorsal and ventral gray matter across the whole section.", "gap": "The V3 section is normalized to a teaching composition; its cellular and whole-cord scales are not consistently calibrated.", "reference_crop_pixels": [ 0, 0, 624, 334 ], "reference_native_size": [ 624, 691 ], "reference_selected_file": "references/selected/25.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/25_cervical_gray_matter_neuronal_distribution.jpg", "model_asset": "m13", "reference_asset": "r25", "full_reference_asset": "f19", "full_figure_file": "reference_figures/PMC4575617_F1.jpg" }, { "number": 26, "group": "04 Spinal cord, brainstem & thalamus", "title": "Cervical gray matter in a Nissl-stained section", "model": "spinal", "model_crop": null, "reference_source": "PMC4575617", "reference_file": "references/PMC4575617/F1.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/925a/4575617/f8d71f50313a/nihms677959f1.jpg", "reference_crop": [ 0, 0.501, 1, 1 ], "reference_sha256": "e9b63a5d029ad5a742a803a69c76b78d690dc6f6b407670d162709e69d2f7eca", "species": "Squirrel monkey", "tissue": "Cervical spinal cord C5", "modality": "Histology", "panel": "Figure 1B; Nissl", "source_caption_title": "Figure 1", "compare": "The second stain provides a different view of cellular architecture in the same spinal region.", "gap": "Matching the butterfly-shaped outline alone does not establish correct laminar packing or motor-pool position.", "reference_crop_pixels": [ 0, 346, 624, 691 ], "reference_native_size": [ 624, 691 ], "reference_selected_file": "references/selected/26.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/26_cervical_gray_matter_in_a_nissl_stained_section.jpg", "model_asset": "m13", "reference_asset": "r26", "full_reference_asset": "f19", "full_figure_file": "reference_figures/PMC4575617_F1.jpg" }, { "number": 27, "group": "04 Spinal cord, brainstem & thalamus", "title": "The cuneate region in an adult human medulla", "model": "medulla", "model_crop": null, "reference_source": "PMC6071077", "reference_file": "references/PMC6071077/cells-07-00072-f003.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/51cf/6071077/46effe304b58/cells-07-00072-g003.jpg", "reference_crop": [ 0, 0, 1, 1 ], "reference_sha256": "4e9dd945721070c51a0dd069ad127266f29570214241cb38f08cb0e255801448", "species": "Human", "tissue": "Adult caudal medulla; dorsal quadrant", "modality": "Immunohistology", "panel": "Figure 3; TRPV1 and Klüver-Barrera", "source_caption_title": "Figure 3", "compare": "Use this reference for regional boundaries around the cuneate nucleus and adjoining structures.", "gap": "The colored V3 relay cluster is not a registered reconstruction of these nuclei or of the actual tract crossing.", "reference_crop_pixels": [ 0, 0, 737, 1572 ], "reference_native_size": [ 737, 1572 ], "reference_selected_file": "references/selected/27.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/27_the_cuneate_region_in_an_adult_human_medulla.jpg", "model_asset": "m14", "reference_asset": "r27", "full_reference_asset": "f20", "full_figure_file": "reference_figures/PMC6071077_cells-07-00072-f003.jpg" }, { "number": 28, "group": "04 Spinal cord, brainstem & thalamus", "title": "Human brainstem relay-cell profiles", "model": "medulla", "model_crop": null, "reference_source": "PMC6071077", "reference_file": "references/PMC6071077/cells-07-00072-f004.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/51cf/6071077/43a0ff5e160c/cells-07-00072-g004.jpg", "reference_crop": [ 0, 0.147, 0.49, 0.291 ], "reference_sha256": "0abc171818ab251fdae8687b2dff851e25e0a9ab36aedeed93af089f48656d98", "species": "Human", "tissue": "Adult human cuneate nucleus", "modality": "Histology", "panel": "Figure 4c; cuneate nucleus, Nissl", "source_caption_title": "Figure 4", "compare": "Compare the real stained soma profiles and surrounding neuropil with modeled relay cells.", "gap": "A Nissl image does not reveal complete dendritic trees; it cannot validate the generator’s full arbor topology.", "reference_crop_pixels": [ 0, 201, 334, 398 ], "reference_native_size": [ 682, 1368 ], "reference_selected_file": "references/selected/28.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/28_human_brainstem_relay_cell_profiles.jpg", "model_asset": "m14", "reference_asset": "r28", "full_reference_asset": "f21", "full_figure_file": "reference_figures/PMC6071077_cells-07-00072-f004.jpg" }, { "number": 29, "group": "04 Spinal cord, brainstem & thalamus", "title": "Measured VPL dendritic reconstructions", "model": "thalamus", "model_crop": null, "reference_source": "PMC11068404", "reference_file": "references/PMC11068404/F0004.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aab1/11068404/f071cc495ed2/jn.00525.2022_f004.jpg", "reference_crop": [ 0, 0, 0.523, 0.654 ], "reference_sha256": "01f72e42ee9791b2da9624b725363ce086c96760cb545c2ceeeca9904c85d92c", "species": "Mouse", "tissue": "VPL and VPM thalamus; juvenile mice", "modality": "Biocytin reconstruction", "panel": "Figure 4A; VPL above, VPM below for contrast", "source_caption_title": "Figure 5", "compare": "VPL cells are shown above; VPM cells below provide a neighboring but different relay population. Compare branching without merging the two nuclei.", "gap": "V3 uses generated relay arbors. Neither mouse population is an imported human VPL reconstruction.", "reference_crop_pixels": [ 0, 0, 408, 424 ], "reference_native_size": [ 781, 649 ], "reference_selected_file": "references/selected/29.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/29_measured_vpl_dendritic_reconstructions.jpg", "model_asset": "m15", "reference_asset": "r29", "full_reference_asset": "f22", "full_figure_file": "reference_figures/PMC11068404_F0004.jpg" }, { "number": 30, "group": "05 Cortex, connectomics & synapses", "title": "A cortical population viewed as individual reconstructed cells", "model": "cortex_close", "model_crop": null, "reference_source": "H01G", "reference_file": "references/h01_gallery_0.png", "reference_image_url": "https://h01-release.storage.googleapis.com/assets/img/gallery/00_l2_interneurons.jpg", "reference_crop": null, "reference_sha256": "d9c5264c610d803cfc1e580900a9f2236265e7a76936b9cd67b928c7fd9df9ab", "species": "Human", "tissue": "H01 temporal cortex; layer 2 interneuron gallery", "modality": "EM reconstruction", "panel": "H01 gallery: layer 2 interneurons", "source_caption_title": "L2 Interneurons A selection of all L2 interneurons that have more than 800 incoming excitatory synapses", "compare": "Compare overlapping arbors and cellular diversity at the population level.", "gap": "V3 repeats ten light-microscopy source morphologies. It is not the dense, independently segmented H01 population.", "reference_crop_pixels": [ 0, 0, 500, 444 ], "reference_native_size": [ 500, 444 ], "reference_selected_file": "references/selected/30.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Human light-microscopy tracing; generated membrane surface", "plate_file": "plates/30_a_cortical_population_viewed_as_individual_reconstructed_cells.jpg", "model_asset": "m16", "reference_asset": "r30", "full_reference_asset": "f23", "full_figure_file": "reference_figures/H01G_h01_gallery_0.png" }, { "number": 31, "group": "05 Cortex, connectomics & synapses", "title": "Cortical layers and cellular distribution", "model": "cortex", "model_crop": null, "reference_source": "PMC11718559", "reference_file": "references/PMC11718559/F4.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/45b5/11718559/b4767b9608e0/nihms-2023839-f0004.jpg", "reference_crop": [ 0, 0, 1, 0.5 ], "reference_sha256": "f4c5dd02fd7f8f340944299ef305f3fbb22f5f6f90997d0f33ab772074fbc880", "species": "Human", "tissue": "H01 temporal cortex", "modality": "EM-derived cell maps", "panel": "Figure 4; upper cellular / vascular maps", "source_caption_title": "Figure 4", "compare": "The source gives a tissue-scale context for neuronal and non-neuronal distributions.", "gap": "V3 shows selected layer groups II, III, and V, not a complete six-layer cellular census or measured cortical slab.", "reference_crop_pixels": [ 0, 0, 987, 525 ], "reference_native_size": [ 987, 1050 ], "reference_selected_file": "references/selected/31.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Human light-microscopy tracing; generated membrane surface", "plate_file": "plates/31_cortical_layers_and_cellular_distribution.jpg", "model_asset": "m17", "reference_asset": "r31", "full_reference_asset": "f24", "full_figure_file": "reference_figures/PMC11718559_F4.jpg" }, { "number": 32, "group": "05 Cortex, connectomics & synapses", "title": "A pyramidal soma and its spiny dendrites", "model": "cell0_soma", "model_crop": null, "reference_source": "PMC11718559", "reference_file": "references/PMC11718559/F5.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/45b5/11718559/3f72a84542cd/nihms-2023839-f0005.jpg", "reference_crop": [ 0, 0.204, 0.49, 0.839 ], "reference_sha256": "42881bafcad3f5524fa0f6903346a2d4b6d6384bc7030ffe94903126c9a936d8", "species": "Human", "tissue": "H01 temporal cortex; different donor / cell", "modality": "EM reconstruction", "panel": "Figure 5D; pyramidal neuron", "source_caption_title": "Figure 5", "compare": "Compare soma-to-dendrite transitions, taper, irregular membrane shape, and visible spine-bearing branches.", "gap": "The left surface is generated around a light-microscopy trace; detailed spines are off and the EM synapse annotations are absent.", "reference_crop_pixels": [ 0, 214, 461, 881 ], "reference_native_size": [ 940, 1050 ], "reference_selected_file": "references/selected/32.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Human light-microscopy tracing; generated membrane surface", "plate_file": "plates/32_a_pyramidal_soma_and_its_spiny_dendrites.jpg", "model_asset": "m18", "reference_asset": "r32", "full_reference_asset": "f25", "full_figure_file": "reference_figures/PMC11718559_F5.jpg" }, { "number": 33, "group": "05 Cortex, connectomics & synapses", "title": "Smooth-dendrite interneuron versus a traced model cell", "model": "cell_1", "model_crop": null, "reference_source": "PMC11718559", "reference_file": "references/PMC11718559/F5.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/45b5/11718559/3f72a84542cd/nihms-2023839-f0005.jpg", "reference_crop": [ 0.495, 0.204, 1, 0.839 ], "reference_sha256": "42881bafcad3f5524fa0f6903346a2d4b6d6384bc7030ffe94903126c9a936d8", "species": "Human", "tissue": "H01 temporal cortex; different cell and specimen", "modality": "EM reconstruction", "panel": "Figure 5E; interneuron", "source_caption_title": "Figure 5", "compare": "The source demonstrates that a realistic cell need not have the same spine pattern as a pyramidal neuron.", "gap": "This is a morphology comparison, not a claim that the left Allen specimen has the right H01 cell’s subtype or connectivity.", "reference_crop_pixels": [ 465, 214, 940, 881 ], "reference_native_size": [ 940, 1050 ], "reference_selected_file": "references/selected/33.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Human light-microscopy tracing; generated membrane surface", "plate_file": "plates/33_smooth_dendrite_interneuron_versus_a_traced_model_cell.jpg", "model_asset": "m19", "reference_asset": "r33", "full_reference_asset": "f25", "full_figure_file": "reference_figures/PMC11718559_F5.jpg" }, { "number": 34, "group": "05 Cortex, connectomics & synapses", "title": "A chandelier-cell reconstruction", "model": "cell_7", "model_crop": null, "reference_source": "H01G", "reference_file": "references/h01_gallery_7.png", "reference_image_url": "https://h01-release.storage.googleapis.com/assets/img/gallery/chandelier.jpg", "reference_crop": null, "reference_sha256": "7cad21669fa8342a8e536eb9309a32e66be4fb6b8a7281fdf4510b880a442802", "species": "Human", "tissue": "H01 temporal cortex; chandelier-cell gallery", "modality": "EM reconstruction", "panel": "H01 gallery: chandelier cell", "source_caption_title": "Chandelier Cell A chandelier cell and some of the pyramidal neurons it inhibits", "compare": "Compare branching organization and the spatial reach of one reconstructed cell.", "gap": "The left source cell is not identified here as a chandelier cell; no matching axonal cartridge topology is claimed.", "reference_crop_pixels": [ 0, 0, 500, 351 ], "reference_native_size": [ 500, 351 ], "reference_selected_file": "references/selected/34.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Human light-microscopy tracing; generated membrane surface", "plate_file": "plates/34_a_chandelier_cell_reconstruction.jpg", "model_asset": "m20", "reference_asset": "r34", "full_reference_asset": "f26", "full_figure_file": "reference_figures/H01G_h01_gallery_7.png" }, { "number": 35, "group": "05 Cortex, connectomics & synapses", "title": "Raw electron microscopy behind a connectomics reconstruction", "model": "cortex_close", "model_crop": null, "reference_source": "PMC11718559", "reference_file": "references/PMC11718559/F2.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/45b5/11718559/a2329f1d59e9/nihms-2023839-f0002.jpg", "reference_crop": [ 0, 0, 0.551, 0.41 ], "reference_sha256": "f806d5890c0bc864dfe582ffc65472ddf58f4838f2bdfa2dfea7fd3ae7b2a201", "species": "Human", "tissue": "H01 temporal cortical neuropil", "modality": "EM + segmentation", "panel": "Figure 2A-B; segmentation examples", "source_caption_title": "Figure 2", "compare": "The source links membrane-defined compartments to segmentation, rather than treating colors as biological boundaries.", "gap": "V3 is surface geometry without a corresponding raw EM volume; there is no voxel-to-membrane validation.", "reference_crop_pixels": [ 0, 0, 579, 252 ], "reference_native_size": [ 1050, 615 ], "reference_selected_file": "references/selected/35.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Human light-microscopy tracing; generated membrane surface", "plate_file": "plates/35_raw_electron_microscopy_behind_a_connectomics_reconstruction.jpg", "model_asset": "m16", "reference_asset": "r35", "full_reference_asset": "f27", "full_figure_file": "reference_figures/PMC11718559_F2.jpg" }, { "number": 36, "group": "05 Cortex, connectomics & synapses", "title": "Neuron surfaces annotated with synaptic inputs", "model": "cell0_soma", "model_crop": null, "reference_source": "H01G", "reference_file": "references/h01_gallery_12.png", "reference_image_url": "https://h01-release.storage.googleapis.com/assets/img/gallery/ei_point.jpg", "reference_crop": null, "reference_sha256": "f419da70cfb271594504eab04a5096efe1e503c9faa10d4b132c4e96abd8b5da", "species": "Human", "tissue": "H01 temporal cortex", "modality": "EM reconstruction + annotations", "panel": "H01 gallery: excitatory / inhibitory synapses", "source_caption_title": "Excitatory/Inhibitory Synapses (Point) Incoming excitatory (yellow) and inhibitory (blue) synapses, rendered as point annotations", "compare": "The points on the reference surface are annotations on reconstructed tissue, not decorative particles.", "gap": "V3 has no experimentally assigned synapse map. Adding dots to the model would not reproduce this evidence.", "reference_crop_pixels": [ 0, 0, 493, 500 ], "reference_native_size": [ 493, 500 ], "reference_selected_file": "references/selected/36.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Human light-microscopy tracing; generated membrane surface", "plate_file": "plates/36_neuron_surfaces_annotated_with_synaptic_inputs.jpg", "model_asset": "m18", "reference_asset": "r36", "full_reference_asset": "f28", "full_figure_file": "reference_figures/H01G_h01_gallery_12.png" }, { "number": 37, "group": "05 Cortex, connectomics & synapses", "title": "Multiple axon-to-dendrite contacts in reconstructed tissue", "model": "cell0_soma", "model_crop": null, "reference_source": "PMC11718559", "reference_file": "references/PMC11718559/F7.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/45b5/11718559/3ca3a3ee3143/nihms-2023839-f0007.jpg", "reference_crop": [ 0, 0, 0.5, 0.265 ], "reference_sha256": "41d237e0df42bec746acd457cfeddf50f2cf2534f3f42250a0baec927d912f44", "species": "Human", "tissue": "H01 temporal cortex; selected strong connection", "modality": "EM reconstruction", "panel": "Figure 7A; selected eight-contact connection", "source_caption_title": "Figure 7", "compare": "This deliberately selected example shows multiple contacts between an axon and dendrite.", "gap": "The source is not a typical-contact-frequency prior. V3 lacks the measured partner identities and contact geometry.", "reference_crop_pixels": [ 0, 0, 525, 238 ], "reference_native_size": [ 1050, 900 ], "reference_selected_file": "references/selected/37.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Human light-microscopy tracing; generated membrane surface", "plate_file": "plates/37_multiple_axon_to_dendrite_contacts_in_reconstructed_tissue.jpg", "model_asset": "m18", "reference_asset": "r37", "full_reference_asset": "f29", "full_figure_file": "reference_figures/PMC11718559_F7.jpg" }, { "number": 38, "group": "05 Cortex, connectomics & synapses", "title": "A real thalamocortical synapse in thin section", "model": "cell0_soma", "model_crop": null, "reference_source": "PMC6946031", "reference_file": "references/PMC6946031/bhx187F3.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/24d4/6946031/42987b5d8707/bhx187f03.jpg", "reference_crop": [ 0, 0, 1, 1 ], "reference_sha256": "bd445abd415c5010f4f87ae8e3af0d5bdd693cbe0e5bf4e0dd83c819e1f7eb81", "species": "Mouse", "tissue": "VPM-to-barrel-cortex pathway; whisker system", "modality": "Transmission EM", "panel": "Figure 3; synaptic contacts", "source_caption_title": "Figure 3.", "compare": "Compare the nanoscale membrane apposition with what the model’s smooth neurite surfaces can actually represent.", "gap": "Synaptic clefts, postsynaptic densities, vesicles, and organelles are not resolved by the V3 source-cell surface.", "reference_crop_pixels": [ 0, 0, 668, 668 ], "reference_native_size": [ 668, 668 ], "reference_selected_file": "references/selected/38.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Human light-microscopy tracing; generated membrane surface", "plate_file": "plates/38_a_real_thalamocortical_synapse_in_thin_section.jpg", "model_asset": "m18", "reference_asset": "r38", "full_reference_asset": "f30", "full_figure_file": "reference_figures/PMC6946031_bhx187F3.jpg" }, { "number": 39, "group": "05 Cortex, connectomics & synapses", "title": "Bouton shape, vesicles, and mitochondria in three dimensions", "model": "cell0_soma", "model_crop": null, "reference_source": "PMC6946031", "reference_file": "references/PMC6946031/bhx187F5.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/24d4/6946031/3ec394e4d65e/bhx187f05.jpg", "reference_crop": [ 0, 0.274, 1, 1 ], "reference_sha256": "ca2ed8c25132dc174a920628c5e200ff718b1b15350741d90260a47c570d95dd", "species": "Mouse", "tissue": "VPM thalamocortical boutons in barrel cortex", "modality": "Serial TEM reconstruction", "panel": "Figure 5B-F; reconstructed boutons", "source_caption_title": "Figure 5.", "compare": "The source separates the bouton envelope from internal structures and postsynaptic contact regions.", "gap": "This is a detail target beyond current model resolution, not a scale-matched comparison of complete cells.", "reference_crop_pixels": [ 0, 346, 713, 1264 ], "reference_native_size": [ 713, 1264 ], "reference_selected_file": "references/selected/39.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Human light-microscopy tracing; generated membrane surface", "plate_file": "plates/39_bouton_shape_vesicles_and_mitochondria_in_three_dimensions.jpg", "model_asset": "m18", "reference_asset": "r39", "full_reference_asset": "f31", "full_figure_file": "reference_figures/PMC6946031_bhx187F5.jpg" }, { "number": 40, "group": "05 Cortex, connectomics & synapses", "title": "Longitudinal axon segments and their bouton organization", "model": "nerve_fibers", "model_crop": null, "reference_source": "PMC6946031", "reference_file": "references/PMC6946031/bhx187F7.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/24d4/6946031/eef42018424e/bhx187f07.jpg", "reference_crop": [ 0, 0, 1, 0.67 ], "reference_sha256": "9587ba23999e2bb924436a9a74743c656a225165043210b5ace07545eaeec801", "species": "Mouse", "tissue": "Cortical thalamocortical axons; not peripheral nerve", "modality": "FIB-SEM reconstruction", "panel": "Figure 7A; segmented axonal excerpts", "source_caption_title": "Figure 7.", "compare": "Compare changes along a neurite instead of assuming one smooth, uniform shaft.", "gap": "The left is a peripheral-fiber model. CNS bouton morphology must not be added indiscriminately to peripheral nerve shafts.", "reference_crop_pixels": [ 0, 0, 800, 639 ], "reference_native_size": [ 800, 954 ], "reference_selected_file": "references/selected/40.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/40_longitudinal_axon_segments_and_their_bouton_organization.jpg", "model_asset": "m10", "reference_asset": "r40", "full_reference_asset": "f32", "full_figure_file": "reference_figures/PMC6946031_bhx187F7.jpg" }, { "number": 41, "group": "06 Neuromuscular junction", "title": "Human motor endplates across lower-limb muscles", "model": "nmj_terminal", "model_crop": null, "reference_source": "PMC5723673", "reference_file": "references/PMC5723673/fig1.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3324/5723673/e7e59602ed28/gr1.jpg", "reference_crop": [ 0, 0.23, 1, 0.45 ], "reference_sha256": "55f327ca2646aeb95c86ecb8ffcb008b2646cb6fd335bcb331c45dcccfa76501", "species": "Human", "tissue": "Lower-limb muscles; not index-finger muscle targets", "modality": "Confocal microscopy", "panel": "Figure 1A; human NMJ rows", "source_caption_title": "Figure 1", "compare": "Compare terminal branching, separate receptor domains, and irregular endplate shape.", "gap": "The V3 terminal is still bead-like and schematic. Human source geometry should replace, not merely decorate, that template.", "reference_crop_pixels": [ 0, 283, 771, 554 ], "reference_native_size": [ 771, 1231 ], "reference_selected_file": "references/selected/41.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/41_human_motor_endplates_across_lower_limb_muscles.jpg", "model_asset": "m21", "reference_asset": "r41", "full_reference_asset": "f33", "full_figure_file": "reference_figures/PMC5723673_fig1.jpg" }, { "number": 42, "group": "06 Neuromuscular junction", "title": "Human NMJs across adult decades", "model": "nmj_terminal", "model_crop": null, "reference_source": "PMC5723673", "reference_file": "references/PMC5723673/fig2.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3324/5723673/96f18001865d/gr2.jpg", "reference_crop": [ 0, 0, 1, 0.52 ], "reference_sha256": "11e354b4d55cf4bcb624989e3e4a342d772f8a60ee590f5983116b129f3bbcd8", "species": "Human", "tissue": "Peroneus longus; adult age groups", "modality": "Confocal microscopy", "panel": "Figure 2A; adult decades", "source_caption_title": "Figure 2", "compare": "The source offers multiple actual human junctions rather than one canonical endplate shape.", "gap": "V3 contains one generated terminal example; it does not encode this between-sample variation or an age-dependent model.", "reference_crop_pixels": [ 0, 0, 736, 339 ], "reference_native_size": [ 736, 651 ], "reference_selected_file": "references/selected/42.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/42_human_nmjs_across_adult_decades.jpg", "model_asset": "m21", "reference_asset": "r42", "full_reference_asset": "f34", "full_figure_file": "reference_figures/PMC5723673_fig2.jpg" }, { "number": 43, "group": "06 Neuromuscular junction", "title": "Presynaptic protein organization below conventional resolution", "model": "nmj_terminal", "model_crop": null, "reference_source": "PMC5723673", "reference_file": "references/PMC5723673/fig3.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3324/5723673/0f24d58a21ac/gr3.jpg", "reference_crop": [ 0, 0, 0.293, 0.625 ], "reference_sha256": "55515bee82d2b8aab8c6ae35f2f4cf126f6679c70a7736404c136fdb884137e3", "species": "Human", "tissue": "Lower-limb NMJ; presynaptic compartment", "modality": "Super-resolution fluorescence", "panel": "Figure 3a; human dSTORM panel", "source_caption_title": "Figure 3", "compare": "The reference resolves molecular labeling within a small presynaptic region.", "gap": "The left terminal surface has no molecular localization data. Its dots or swellings should not be interpreted as protein clusters.", "reference_crop_pixels": [ 0, 0, 220, 238 ], "reference_native_size": [ 750, 380 ], "reference_selected_file": "references/selected/43.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/43_presynaptic_protein_organization_below_conventional_resolution.jpg", "model_asset": "m21", "reference_asset": "r43", "full_reference_asset": "f35", "full_figure_file": "reference_figures/PMC5723673_fig3.jpg" }, { "number": 44, "group": "06 Neuromuscular junction", "title": "Species differences matter at the motor endplate", "model": "nmj_close", "model_crop": null, "reference_source": "PMC7542190", "reference_file": "references/PMC7542190/joa13260-fig-0002.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eeba/7542190/2939a8e4ad23/JOA-237-827-g002.jpg", "reference_crop": [ 0, 0, 1, 1 ], "reference_sha256": "3f50e38dc0df50851df04f9e304b22b7f1add3611763f0d1e36b6bdb400a62de", "species": "Multiple species", "tissue": "Human, mouse, cat, dog, sheep, and pig NMJs", "modality": "Confocal microscopy", "panel": "Figure 2; species comparison", "source_caption_title": "FIGURE 2", "compare": "Compare the different terminal and receptor patterns across species in the source montage.", "gap": "Do not copy the most familiar mouse endplate shape into a human model without labeling the substitution.", "reference_crop_pixels": [ 0, 0, 709, 188 ], "reference_native_size": [ 709, 188 ], "reference_selected_file": "references/selected/44.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/44_species_differences_matter_at_the_motor_endplate.jpg", "model_asset": "m22", "reference_asset": "r44", "full_reference_asset": "f36", "full_figure_file": "reference_figures/PMC7542190_joa13260-fig-0002.jpg" }, { "number": 45, "group": "07 Proprioceptive endings", "title": "A spindle inside a real muscle cross-section", "model": "spindle", "model_crop": [ 0.22, 0, 0.63, 1 ], "reference_source": "PMC4811329", "reference_file": "references/PMC4811329/F1.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/88ef/4811329/dbcb886819fd/emss-32827-f0001.jpg", "reference_crop": null, "reference_sha256": "21ca5e41510cad64277ecf61932cbc9cbee2790233ddf19e88db487c0ce6f19d", "species": "Sheep", "tissue": "Extraocular muscle spindle; not a finger-muscle specimen", "modality": "Histology", "panel": "Figure 1; spindle section", "source_caption_title": "Figure 1", "compare": "The section shows intrafusal fibers, capsule, and surrounding extrafusal tissue together.", "gap": "V3 has a simplified longitudinal comparison specimen; its capsule and intrafusal architecture are not fitted to this section.", "reference_crop_pixels": [ 0, 0, 800, 707 ], "reference_native_size": [ 800, 707 ], "reference_selected_file": "references/selected/45.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/45_a_spindle_inside_a_real_muscle_cross_section.jpg", "model_asset": "m23", "reference_asset": "r45", "full_reference_asset": "f37", "full_figure_file": "reference_figures/PMC4811329_F1.jpg" }, { "number": 46, "group": "07 Proprioceptive endings", "title": "Spindle sensory terminals among intrafusal fibers", "model": "spindle_detail", "model_crop": [ 0.22, 0, 0.63, 1 ], "reference_source": "PMC4811329", "reference_file": "references/PMC4811329/F3.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/88ef/4811329/864213679f9f/emss-32827-f0003.jpg", "reference_crop": [ 0, 0.33, 0.5, 1 ], "reference_sha256": "d4d83662b0bc527a52fb5c7cb10d9b46c499392805601c5ef59218d72a2be603", "species": "Sheep", "tissue": "Extraocular muscle spindle; equatorial region", "modality": "Confocal microscopy", "panel": "Figure 3C,E; sensory region", "source_caption_title": "Figure 3", "compare": "Compare wrapping and branching around individual intrafusal fibers with the repeated model helices.", "gap": "The repeated geometry is too regular to stand in for individually traced endings and their associated supporting cells.", "reference_crop_pixels": [ 0, 288, 400, 872 ], "reference_native_size": [ 800, 872 ], "reference_selected_file": "references/selected/46.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/46_spindle_sensory_terminals_among_intrafusal_fibers.jpg", "model_asset": "m24", "reference_asset": "r46", "full_reference_asset": "f38", "full_figure_file": "reference_figures/PMC4811329_F3.jpg" }, { "number": 47, "group": "07 Proprioceptive endings", "title": "A spindle’s sensory interface under electron microscopy", "model": "spindle_detail", "model_crop": [ 0.22, 0, 0.63, 1 ], "reference_source": "PMC4811329", "reference_file": "references/PMC4811329/F2.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/88ef/4811329/fad663c92ffb/emss-32827-f0002.jpg", "reference_crop": [ 0, 0, 1, 1 ], "reference_sha256": "7f76f43e7baa111787fb0833084ffe15657cb21123505bc32eda619f43892d72", "species": "Sheep", "tissue": "Extraocular muscle spindle", "modality": "Transmission EM", "panel": "Figure 2; capsule and sensory / motor contacts", "source_caption_title": "Figure 2", "compare": "The micrographs separate the capsule, sensory endings, motor ending, and muscle-fiber interfaces.", "gap": "The model does not contain the organelles, basal-lamina relationships, or synaptic ultrastructure visible here.", "reference_crop_pixels": [ 0, 0, 800, 700 ], "reference_native_size": [ 800, 700 ], "reference_selected_file": "references/selected/47.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/47_a_spindle_s_sensory_interface_under_electron_microscopy.jpg", "model_asset": "m24", "reference_asset": "r47", "full_reference_asset": "f39", "full_figure_file": "reference_figures/PMC4811329_F2.jpg" }, { "number": 48, "group": "07 Proprioceptive endings", "title": "Golgi tendon-organ afferents in a whole-mount preparation", "model": "golgi_detail", "model_crop": [ 0.32, 0, 0.81, 1 ], "reference_source": "PMC4811329", "reference_file": "references/PMC4811329/F5.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/88ef/4811329/22bd613ec219/emss-32827-f0005.jpg", "reference_crop": [ 0, 0, 0.494, 0.498 ], "reference_sha256": "705688054bf65a1bae6ce94cf39f6ec7c0fb1cdb24e023db13bced273a1dc996", "species": "Sheep", "tissue": "Extraocular muscle tendon organ", "modality": "Confocal microscopy", "panel": "Figure 5A; whole-mount GTO", "source_caption_title": "Figure 5", "compare": "The source shows an afferent entering and branching within an actual tendon-organ preparation.", "gap": "V3 uses a generated arbor alongside generic collagen strands. This is a cross-muscle, cross-species morphology analogue.", "reference_crop_pixels": [ 0, 0, 395, 314 ], "reference_native_size": [ 800, 630 ], "reference_selected_file": "references/selected/48.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/48_golgi_tendon_organ_afferents_in_a_whole_mount_preparation.jpg", "model_asset": "m25", "reference_asset": "r48", "full_reference_asset": "f40", "full_figure_file": "reference_figures/PMC4811329_F5.jpg" }, { "number": 49, "group": "07 Proprioceptive endings", "title": "Tendon-organ capsule and collagen relationships", "model": "golgi_tendon", "model_crop": [ 0.32, 0, 0.81, 1 ], "reference_source": "PMC4811329", "reference_file": "references/PMC4811329/F4.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/88ef/4811329/5c37e1c28b1a/emss-32827-f0004.jpg", "reference_crop": [ 0, 0, 0.494, 0.491 ], "reference_sha256": "9b35b4914391001f947bc9445f2b5b251c3e817c57811e2345b37d42eb818455", "species": "Sheep", "tissue": "Extraocular muscle tendon organ", "modality": "Histology", "panel": "Figure 4A; Azan-stained section", "source_caption_title": "Figure 4", "compare": "Compare the capsule and collagen-filled interior with the open longitudinal model.", "gap": "A realistic tendon organ needs the terminal embedded within its actual collagen architecture, not simply beside parallel strands.", "reference_crop_pixels": [ 0, 0, 395, 346 ], "reference_native_size": [ 800, 705 ], "reference_selected_file": "references/selected/49.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/49_tendon_organ_capsule_and_collagen_relationships.jpg", "model_asset": "m26", "reference_asset": "r49", "full_reference_asset": "f41", "full_figure_file": "reference_figures/PMC4811329_F4.jpg" }, { "number": 50, "group": "07 Proprioceptive endings", "title": "Tendon-organ endings between collagen fibrils", "model": "golgi_detail", "model_crop": [ 0.32, 0, 0.81, 1 ], "reference_source": "PMC4811329", "reference_file": "references/PMC4811329/F4.jpg", "reference_image_url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/88ef/4811329/5c37e1c28b1a/emss-32827-f0004.jpg", "reference_crop": [ 0, 0.5, 1, 1 ], "reference_sha256": "9b35b4914391001f947bc9445f2b5b251c3e817c57811e2345b37d42eb818455", "species": "Sheep", "tissue": "Extraocular muscle tendon organ", "modality": "Transmission EM", "panel": "Figure 4C-D; terminal / collagen contacts", "source_caption_title": "Figure 4", "compare": "The source resolves terminals within collagen and the local supporting-cell relationship.", "gap": "The model has no fibril-scale packing, membrane contacts, or corresponding mechanical coupling.", "reference_crop_pixels": [ 0, 352, 800, 705 ], "reference_native_size": [ 800, 705 ], "reference_selected_file": "references/selected/50.jpg", "scale_notice": "Independent image magnifications; not a matched field, specimen, or common scale. See source figure for reference scale bars.", "model_notice": "Actual unchanged V3 geometry; camera/visibility changes only. Screen-only neurite visibility padding on; modeled spines/boutons off.", "model_basis": "Synthetic anatomical specimen; literature-informed model priors", "plate_file": "plates/50_tendon_organ_endings_between_collagen_fibrils.jpg", "model_asset": "m25", "reference_asset": "r50", "full_reference_asset": "f41", "full_figure_file": "reference_figures/PMC4811329_F4.jpg" } ] }