Academic Journal
A curvilinear coordinate flatmap for visualizing hippocampal structure and development.
| Τίτλος: | A curvilinear coordinate flatmap for visualizing hippocampal structure and development. |
|---|---|
| Συγγραφείς: | Bhandiwad AA; Allen Institute for Brain Science, Seattle, WA., Kronman F; Department of Neuroscience and Experimental Therapeutics, College of Medicine, The Pennsylvania State University, Hershey, PA., Liwang J; Department of Neuroscience and Experimental Therapeutics, College of Medicine, The Pennsylvania State University, Hershey, PA., Gao P; Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA., Rossant C; University College London, London, UK.; International Brain Laboratory., Birman D; International Brain Laboratory.; Allen Institute for Neural Dynamics, Seattle, WA., Puelles L; University of Murcia, Murcia, Spain., Ding SL; Allen Institute for Brain Science, Seattle, WA., Xu X; Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA., Ng L; Allen Institute for Brain Science, Seattle, WA., Kim Y; Department of Neuroscience and Experimental Therapeutics, College of Medicine, The Pennsylvania State University, Hershey, PA.; Center for Neural Engineering, The Pennsylvania State University, University Park, PA., Mollenkopf T; Allen Institute for Brain Science, Seattle, WA. |
| Πηγή: | BioRxiv : the preprint server for biology [bioRxiv] 2026 Mar 11. Date of Electronic Publication: 2026 Mar 11. |
| Τύπος έκδοσης: | Journal Article; Preprint |
| Γλώσσα: | English |
| Στοιχεία περιοδικού: | Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE |
| Περίληψη: | The hippocampal formation is a highly curved and topographically complex forebrain structure. This complex geometry presents persistent challenges for analyzing subregional, laminar, and connectivity patterns. Here, we present a computational workflow that generates curvilinear-coordinate flatmaps from Common Coordinate Framework (CCF) registered hippocampal and retrohippocampal regions by solving the Laplacian equation to derive geodesic streamlines. This transformation unfolds the hippocampus into a planar slab, bounded by the meningeal and ventricular surfaces, with the depth defined along the radial axis. We apply this transform to image volumes, single neuron reconstructions, and point data, including spatial transcriptomic and rabies tracing datasets, revealing topographic variations in the dorsoventral and radial axes that are obscured in the CCF coordinate space. As proof of principle, we use flatmaps to show connectivity loss in a mouse model of Alzheimer's disease and track postnatal development of microglial distribution in the hippocampus. This work provides an efficient and accessible resource for visualizing hippocampal organization across development and disease, offering new opportunities to interrogate the structure and function of this important brain region. |
| References: | Trends Neurosci. 2013 Oct;36(10):570-8. (PMID: 23871546) Methods. 2010 Feb;50(2):55-62. (PMID: 19818854) Science. 2011 Sep 9;333(6048):1456-8. (PMID: 21778362) Science. 2000 Dec 22;290(5500):2319-23. (PMID: 11125149) J Comp Neurol. 1978 Oct 15;181(4):681-715. (PMID: 690280) Imaging Neurosci (Camb). 2024 Jun 28;2:. (PMID: 40800415) Neuroscience. 2005;134(1):107-20. (PMID: 15961234) J Comp Neurol. 1980 May 15;191(2):255-81. (PMID: 7410593) Neuroimage. 2011 Feb 1;54(3):2033-44. (PMID: 20851191) Brain Res Bull. 1997;44(2):107-12. (PMID: 9292198) Cell. 2017 Oct 5;171(2):456-469.e22. (PMID: 28985566) PLoS Biol. 2023 Jun 30;21(6):e3002133. (PMID: 37390046) Physiol Rev. 2022 Jan 1;102(1):343-378. (PMID: 34280053) Cell. 2020 May 14;181(4):936-953.e20. (PMID: 32386544) Neuroimage. 2012 Aug 15;62(2):911-22. (PMID: 22248580) J Comp Neurol. 1990 May 22;295(4):580-623. (PMID: 2358523) Neuron. 2010 Jan 14;65(1):7-19. (PMID: 20152109) Nat Methods. 2023 Feb;20(2):229-238. (PMID: 36587187) Sci Adv. 2024 Oct 11;10(41):eado8837. (PMID: 39392880) Neuroimage. 2011 Apr 15;55(4):1435-42. (PMID: 21256229) Nature. 2021 Oct;598(7879):174-181. (PMID: 34616072) Curr Biol. 2015 Dec 7;25(23):R1116-21. (PMID: 26654366) Neuroimage. 2018 Feb 15;167:408-418. (PMID: 29175494) Hum Brain Mapp. 2000 Sep;11(1):12-32. (PMID: 10997850) J Neurosci Methods. 1992 Mar;41(3):255-67. (PMID: 1513183) Cell Rep. 2022 Jun 21;39(12):110978. (PMID: 35732133) Neuroscience. 1989;31(3):571-91. (PMID: 2687721) J Comp Neurol. 1994 Jan 8;339(2):181-208. (PMID: 8300905) Brain Res Rev. 2007 Nov;56(1):1-26. (PMID: 17559940) Nature. 2023 Dec;624(7991):343-354. (PMID: 38092912) Sci Data. 2023 Jul 26;10(1):486. (PMID: 37495585) J Physiol. 1998 Feb 15;507 ( Pt 1):219-36. (PMID: 9490842) Nat Methods. 2025 Apr;22(4):861-873. (PMID: 40119176) J Comp Neurol. 2021 Feb;529(3):576-594. (PMID: 32511750) Hippocampus. 2023 Sep;33(9):1028-1047. (PMID: 37280038) Neuroimage. 2022 May 1;251:118987. (PMID: 35151850) Neuroimage. 2023 Aug 1;276:120182. (PMID: 37230208) Nat Rev Neurosci. 2024 Jun;25(6):414-427. (PMID: 38658739) Prog Neurobiol. 1989;33(3):161-253. (PMID: 2682783) Science. 2024 Feb 2;383(6682):eadj9198. (PMID: 38300992) Science. 2022 Nov 4;378(6619):488-492. (PMID: 36378966) Neuron. 2014 Jul 16;83(2):309-323. (PMID: 24952961) J Comp Neurol. 2023 Jul;531(10):1008-1016. (PMID: 37002855) Nat Methods. 2021 Nov;18(11):1342-1351. (PMID: 34711970) Cell Rep. 2023 May 30;42(5):112425. (PMID: 37099424) Hippocampus. 2003;13(1):133-49. (PMID: 12625464) Nat Commun. 2024 Oct 21;15(1):9072. (PMID: 39433760) Nature. 2014 Apr 10;508(7495):207-14. (PMID: 24695228) J Comp Neurol. 2019 Jul 1;527(10):1731-1752. (PMID: 30737959) Glia. 2007 Oct;55(13):1334-47. (PMID: 17647290) Front Neural Circuits. 2024 Jul 10;18:1398884. (PMID: 39050044) Nat Commun. 2025 Oct 29;16(1):9538. (PMID: 41162351) Nat Methods. 2023 Nov;20(11):1822-1829. (PMID: 37783883) Nat Rev Neurosci. 2014 Oct;15(10):655-69. (PMID: 25234264) Nature. 2023 Dec;624(7991):317-332. (PMID: 38092916) Proc Natl Acad Sci U S A. 2020 Feb 11;117(6):3220-3231. (PMID: 31988117) Nat Commun. 2024 Jul 30;15(1):6398. (PMID: 39080289) Neuroimage. 1999 Feb;9(2):195-207. (PMID: 9931269) Nature. 2019 Nov;575(7781):195-202. (PMID: 31666704) J Comp Neurol. 1980 Mar 1;190(1):115-34. (PMID: 7381049) |
| Grant Information: | U01 AG076791 United States AG NIA NIH HHS |
| Entry Date(s): | Date Created: 20260209 Date Completed: 20260325 Latest Revision: 20260920 |
| Update Code: | 20260920 |
| PubMed Central ID: | PMC12873774 |
| DOI: | 10.64898/2026.01.29.702633 |
| PMID: | 41659659 |
| Βάση Δεδομένων: | MEDLINE |
| ISSN: | 2692-8205 |
|---|---|
| DOI: | 10.64898/2026.01.29.702633 |