Citations and credits

Every dataset behind this site: who made it, what licence it carries, and which page uses it. This page was created by Amy Sterling as an extension of connectome.quest Neuro 101 and Connectome 101.

If you use any of this

Cite the people who made the data, not this site. Every reference below is the one its authors asked for.

Reference guides

Two pages carry written reference guides beneath their instruments, with sources cited inline: pain, from receptor to treatment, and the sensorimotor cortex.

The sources

Each number is a direct link to that reference. The context links beneath it show which pages draw from the source.

1. #1

   Europe PMC Consortium, Nucleic Acids Res 43:D1042 (2015), doi:10.1093/nar/gku1061. Full text availability and preprint index queried through the public REST API.

   Bibliographic records from Europe PMC, free to use. · used on The reading list

2. #2

   Reference lists from Europe PMC (Europe PMC Consortium, Nucleic Acids Res 43:D1042, 2015, doi:10.1093/nar/gku1061).

   Bibliographic records from Europe PMC, free to use. · used on The reading list

3. #3

   Europe PMC Consortium. Europe PMC: a full-text literature database for the life sciences. Nucleic Acids Res 43:D1042 (2015), doi:10.1093/nar/gku1061. Queried through the public REST API.

   Bibliographic records from Europe PMC, free to use; each paper carries its own licence at its publisher. · used on The reading list · Deep structure pages

4. #4

   Borner K, et al. Human Reference Atlas. Nature Methods (2025). Geometry derives from the Allen Human Reference Atlas 3D, Ding et al.

   CC BY 4.0 · the data · used on From Earth to a synapse

5. #5

   Faizy TD, Kumar D, Broocks G, et al. Age-related measures of the human brain's white matter myelin. Sci Rep 8, 14991 (2018). doi.org/10.1038/s41598-018-33112-8

   CC BY 4.0 · the data · used on Microseconds to decades

6. #6

   Hafting T, Fyhn M, Molden S, Moser M-B, Moser EI. Microstructure of a spatial map in the entorhinal cortex. Nature 436:801–806 (2005), doi:10.1038/nature03721; dataset doi:10.11582/2017.00017.

   CC BY 4.0 · the data · used on Deep structure pages

7. #7

   MNI152NLin2009cAsym brain mask, via TemplateFlow. Fonov V, et al. Unbiased average age-appropriate atlases for pediatric studies. NeuroImage 54, 313 (2011).

   CC BY 4.0 · the data · used on The white matter

8. #8

   Pauli WM, Nili AN, Tyszka JM. A high-resolution probabilistic in vivo atlas of human subcortical brain nuclei. Scientific Data 5:180063 (2018). doi:10.1038/sdata.2018.63.

   CC BY 4.0 · the data · used on Deep structure pages

9. #9

   Shapson-Coe et al., Science 384, eadk4858 (2024)

   CC BY 4.0 · used on A cubic millimetre · From Earth to a synapse

10. #10

    Ye, et al. Brain-wide topographic coordination of rotating waves. Science 392, eadx1369 (2026). doi:10.1126/science.adx1369. Widefield calcium imaging in mice: rotating waves centred on somatosensory cortex, sweeping across the somatotopic maps, mirrored between hemispheres.

    CC BY 4.0 (Figshare data); analysis code at github.com/zhiwen10/YE-et-al-2023-spirals carries no licence file · the data · used on Spiral waves

11. #11

    Amunts K, Lepage C, Borgeat L, et al. BigBrain: An Ultrahigh-Resolution 3D Human Brain Model. Science 340, 1472 (2013). (CC BY-NC-SA 4.0). No citation is recorded upstream.

    CC BY-NC-SA 4.0 · the data · used on From Earth to a synapse

12. #12

    BodyParts3D / Anatomography, The Database Center for Life Science, Japan (release 3.0): polygon models of one adult male, 22 skull bones merged. Mitsuhashi N et al., BodyParts3D: 3D structure database for anatomical concepts, Nucleic Acids Research 37:D782 (2009).

    CC BY-SA 2.1 JP · used on Somatotopy

13. #13

    BodyParts3D, The Database Center for Life Science (DBCLS). Mitsuhashi N, et al. BodyParts3D: 3D structure database for anatomical concepts. Nucleic Acids Res 37, D782 (2009). (CC BY-SA 2.1 Japan). No citation is recorded upstream.

    CC BY-SA 2.1 Japan · the data · used on From Earth to a synapse

14. #14

    Najdenovska E, Aleman-Gomez Y, Battistella G, Descoteaux M, Hagmann P, Jacquemont S, Maeder P, Thiran J-P, Fornari E, Bach Cuadra M. In-vivo probabilistic atlas of human thalamic nuclei based on diffusion weighted magnetic resonance imaging. Scientific Data 5:180270 (2018).

    CC BY-SA 4.0 · the data · used on Deep structure pages

15. #15

    Yeh FC, Population-based tract-to-region connectome of the human brain. Nat Commun 13, 4933 (2022).

    CC-BY-SA 4.0 · the data · used on From Earth to a synapse · Pain · Deep structure pages · Somatotopy · The white matter

16. #16

    Tractography: Yeh FC, Population-based tract-to-region connectome of the human brain. Nat Commun 13, 4933 (2022). Parcellation: Glasser MF et al., Nature 536:171 (2016), on the HCP S1200 group-average midthickness surface, Van Essen et al., NeuroImage 80:62 (2013).

    CC-BY-SA 4.0 (tractography); HCP Open Access Data Use Terms (surface and parcellation) · used on Somatotopy

17. #17

    Lee JJ, Jo S, Cho S, Woo CW. Personalized brain decoding of spontaneous pain in individuals with chronic pain. Nat Neurosci (2026). doi:10.1038/s41593-026-02221-3. Behavioural rating files from OpenNeuro ds006815.

    CC0 · the data · used on Pain

18. #18

    Ma S, Huang T, Qu Y, Chen X, Zhang Y, Zhen Z. An fMRI dataset for whole-body somatotopic mapping in humans. Sci Data 9, 515 (2022). doi:10.1038/s41597-022-01644-4

    CC0 · the data · used on Somatotopy

19. #19

    Mohammadian M et al. Evidence for a role of skull bone marrow in human chronic pain as revealed by TSPO PET imaging. medRxiv 2025.07.19.25331817; peer-reviewed version PMID 41551382. Derivatives from OpenNeuro ds007907.

    CC0 · the data · used on Pain

20. #20

    OpenNeuro ds007095, human stereo EEG.

    CC0 · the data · used on Microseconds to decades

21. #21

    The dataset's own dataset_description.json lists its authors as a TODO placeholder, so there is no paper to cite and nobody named to credit. It is CC0 and the credit is owed to NYU CBI regardless.

    CC0 · the data · used on Retinotopy

22. #22

    Wei Z et al. CoSpine open access simultaneous cortico-spinal fMRI database of thermal pain and motor tasks. Sci Data (2025). doi:10.1038/s41597-025-05982-x. Cord silhouette and vertebral levels from the PAM50 template, De Leener B et al., NeuroImage 165:170 (2018), doi:10.1016/j.neuroimage.2017.10.041, distributed with the Spinal Cord Toolbox.

    CC0 · the data · used on Pain

23. #23

    Whole cell current clamp from human cortical tissue, DANDI dandiset 000293.

    CC0-1.0 · the data · used on Microseconds to decades

24. #24

    Iglesias JE et al. A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution MRI. NeuroImage 115:117–137 (2015). doi:10.1016/j.neuroimage.2015.04.042.

    FreeSurfer Software License Agreement v1.0; full terms in licenses/freesurfer-atlas-license.txt · the data · used on Deep structure pages

25. #25

    Iglesias JE et al. A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology. NeuroImage 183:314–326 (2018). doi:10.1016/j.neuroimage.2018.08.012.

    FreeSurfer Software License Agreement v1.0; full terms in licenses/freesurfer-atlas-license.txt · the data · used on Deep structure pages

26. #26

    Saygin ZM et al. High-resolution magnetic resonance imaging reveals nuclei of the human amygdala. NeuroImage 155:370–382 (2017). doi:10.1016/j.neuroimage.2017.04.046.

    FreeSurfer Software License Agreement v1.0; full terms in licenses/freesurfer-atlas-license.txt · the data · used on Deep structure pages

27. #27

    HCP S1200 group average, Van Essen et al., NeuroImage 80:62 (2013). MSMAll registered.

    HCP Open Access Data Use Terms · the data · used on Pain · Deep structure pages · Somatotopy · Spiral waves · The white matter

28. #28

    Glasser MF et al. A multi-modal parcellation of human cerebral cortex. Nature 536:171 (2016). doi:10.1038/nature18933. Names, lobes and cortex groups from the HCP-MMP1 unique region list compiled by Dianne Patterson, University of Arizona: https://bitbucket.org/dpat/tools/raw/master/REF/ATLASES/HCP-MMP1_UniqueRegionList.csv

    HCP Open Access Data Use Terms (parcellation); region list redistributed with attribution · used on The reading list · Somatotopy

29. #29

    Fonov VS et al. Unbiased average age-appropriate atlases for pediatric studies. NeuroImage 54:313–327 (2011). doi:10.1016/j.neuroimage.2010.07.033.

    MNI template license; full terms in licenses/mni-template-license.txt · the data · used on Deep structure pages

30. #30

    Tian Y, Margulies DS, Breakspear M, Zalesky A. Topographic organization of the human subcortex unveiled with functional connectivity gradients. Nat Neurosci 23:1421 (2020). doi:10.1038/s41593-020-00711-6

    Melbourne Subcortex Atlas licence: use, copy, modify, publish and distribute permitted with citation · the data · used on Pain

31. #31

    Hao H, Ramli R, Wang C, et al. Dorsal root ganglia control nociceptive input to the central nervous system. PLoS Biol 21:e3001958 (2023). doi:10.1371/journal.pbio.3001958. Reconstruction from NeuroMorpho.Org, Gamper archive.

    NeuroMorpho.Org data use terms, citation required · the data · used on Pain

32. #32

    McDermott LA et al. Defining the functional role of NaV1.7 in human nociception. Neuron 101:905 (2019). doi:10.1016/j.neuron.2019.01.047. Reconstruction from NeuroMorpho.Org (Ascoli et al., J Neurosci 27:9247, 2007), Weir archive.

    NeuroMorpho.Org data use terms, citation required · the data · used on Pain

33. #33

    PhysioNet EEG Motor Movement/Imagery Database, subject 1, runs 1 and 2, all 64 channels. Electrode coordinates are the standard 10-05 template (MNE), not this person's head.

    ODC-BY 1.0 · used on Microseconds to decades

34. #34

    Nobel Assembly at Karolinska Institutet. The Nobel Prize in Physiology or Medicine 2014: cells that constitute a positioning system in the brain.

    Official Nobel Prize explanatory source; page copyright applies · the data · used on Deep structure pages

35. #35

    Yarkoni T, Poldrack RA, Nichols TE, Van Essen DC, Wager TD. Large-scale automated synthesis of human functional neuroimaging data. Nat Methods 8:665 (2011), doi:10.1038/nmeth.1635. Database version 7, github.com/neurosynth/neurosynth-data.

    Open Database License (ODbL) 1.0, share-alike: this derived file is released under the same licence and stays open. Deep-structure masks from the Melbourne Subcortex Atlas (Tian Y et al., Nat Neurosci 23:1421, 2020), cortical parcels from Glasser MF et al., Nature 536:171 (2016). · used on The reading list · Deep structure pages · Somatotopy

36. #36

    Blue Marble and city lights: NASA Earth Observatory / NASA Worldview (GIBS). Satellite frames: NASA GIBS, MODIS on Terra. Aerial: USGS National Agriculture Imagery Program, 1 m.

    Public domain (NASA and USGS) · used on From Earth to a synapse

37. #37

    Xu, Y., Long, X., Feng, J., Gong, P. Interacting spiral wave patterns underlie complex brain dynamics and are related to cognitive processing. Nature Human Behaviour 7 (2023). doi:10.1038/s41562-023-01626-5. Spiral waves detected in HCP resting and task fMRI, 100 subjects, fs_LR 32k, 0.01 to 0.1 Hz BOLD phase.

    Raw inputs are HCP data behind ConnectomeDB data use terms and cannot be redistributed here; no derived maps are shipped by the authors; toolbox at github.com/BrainDynamicsUSYD/BrainVortexToolbox carries no licence file · the data · used on Spiral waves

38. #38

    Hand-picked by the site's authors from the most-cited papers whose title names each region; every DOI checked against Crossref by scripts/validate_region_reading.py.

    This list is editorial, CC BY 4.0 like the rest of the site's prose. Each paper carries its own licence at its publisher. · used on The reading list · Deep structure pages · Somatotopy

39. #39

    Burgess N, Cacucci F, Lever C, O'Keefe J. Characterizing multiple independent behavioral correlates of cell firing in freely moving animals. Hippocampus 15:149–153 (2005). doi:10.1002/hipo.20058.

    UCL article supplementary sample; no reuse licence stated on the resource page · the data · used on Deep structure pages

40. #40

    Tian Y et al. Topographic organization of the human subcortex unveiled with functional connectivity gradients. Nature Neuroscience 23:1421–1432 (2020). doi:10.1038/s41593-020-00711-6.

    Use, modification, publication and distribution permitted with citation; see the Melbourne Subcortex Atlas license · the data · used on Deep structure pages

41. #41

    Deep structure pages: hand-curated text with primary sources listed on each page, from Scoville and Milner, J Neurol Neurosurg Psychiatry 1957 to Tian et al., Nat Neurosci 2020. Anatomy meshes from the Melbourne Subcortex Atlas, Tian Y et al., Nat Neurosci 23:1421 (2020), doi:10.1038/s41593-020-00711-6.

    text CC-BY 4.0 like the rest of the site's prose · the data

42. #42

    Relay chains distilled from published tracing, imaging and review literature, cited per chain in each chain's citations list; parcels HCP-MMP1 (Glasser et al., Nature 2016), deep structures Melbourne Subcortex Atlas (Tian et al., Nature Neuroscience 2020), measured bundles HCP1065 population atlas (Yeh 2022, NeuroImage).

    see the source · used on Circuits of the brain · Somatotopy

Licences worth knowing about

Most of what is here is free for any use. Two things are not, and they are flagged above: 1 dataset carries a noncommercial clause, and 8 carry share-alike, which means anything derived from them inherits the same terms. If this site is ever licensed commercially, those are the parts that have to come out.

Tools

Built with three.js, CloudVolume, trimesh, MNE-Python, NiBabel, scikit-image, NumPy and SciPy.