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Sudha Gopalakrishnan Brain Centre

Indian Institute of Technology Madras

ANCHOR: Atlas of Neurochemical Characterization of the Human brainstem with 3D<br>Reconstruction

Abstract

The human brainstem is a complex division of the brain comprised of more than 200 nuclei and fiber tracts. The brainstem is essential for the functioning of the entire body. We introduce here the most detailed human brainstem Atlas across the human lifespan: fetus, child, adult. ANCHOR, the Atlas of Neurochemical Characterization of the Human Brainstem, is an online platform that includes more than 800 serial histological sections, stained for Nissl and seven immunochemical (IHC) markers, from the human brainstem of three ages: 25 fetal gestational weeks (GW), 9 years old, and 54 years old. This makes ANCHOR the most comprehensive human brainstem Atlas to date. In these three brainstems, we identified and manually annotated over 200 structures. We further characterized these structures with the seven IHC markers. We specifically describe the catecholaminergic groups in the human brainstem across all three age groups. In addition, we identified the protoplasmic commissural dendrites of the hypoglossal nucleus and we describe the pretectal nuclei in the Nissl-stained fetal 25 GW brainstem. ANCHOR includes an online viewer that integrates multimodal data, from magnetic resonance imaging and block face imaging to Nissl- and IHC-stained serial sections and 3D reconstruction of the entire brainstem. For the 9-year-old specimen, the online viewer allows simultaneous navigation of annotated sections with corresponding IHC, for viewing the specific region-wise cellular features accessible at<br>https://anchor.humanbrain.in/.

Mihail Bota, Soundharya Venkatesh, Shevani Arun Arunesh, Nagajothi Ganesan, Supriti Mulay, Karan Ramana Gopi, Sruti Rekha Muni, Shrimathi Mani, Chrisline Sam C, A.S.T. Aditya Bharg, Vinoth Kanna G, Rajeswaran Rangaswami, S. Lata, E. Harish Kumar, S. Suresh, Mousumi Sen, Ranjit Immanuel James, Abi Manesh, George M. Varghese, K.V. Vinoth, Keerthi Ram, Richa Verma, Paul R. Manger, Mohanasankar Sivaprakasam<br>(2026), ANCHOR: Atlas of Neurochemical Characterization of the Human brainstem with 3D Reconstruction. bioRxiv 2026.06.03.727794; doi:<br>https://doi.org/10.64898/2026.06.03.727794

Authors

Richa Verma, Mihail Bota, Keerthi Ram, Jaikishan Jaykumar, Rebecca Folkerth,<br>Karthika Pandurangan, Jivitha Jyothi Ramesh, Moitrayee Majumder, Rakshika<br>Raveendran, Reetuparna Nanda, Sivamani K, Amal Dhivahar S, Srinivasa Karthik,<br>Ramdayalan Kumarasami, Suresh S, S. Lata, E. Harish Kumar, Rajeswaran<br>Rangasami, Chitra Srinivasan, Jayaraman Kumutha, Sudha Vasudevan, Koushik Bhat,<br>Chrisline Sam C, Sivathanu Neelakantan, Stephen Savoia, Partha P Mitra, Jayaraj<br>Joseph, Paul Manger, Mohanasankar Sivaprakasam.

Abstract

We introduce DHARANI, an online platform that features the first 3D histological reconstruction<br>of the developing human brain during the second trimester spanning 14-24 gestational weeks<br>(GW). This novel digital repository bridges the gap from sections to volumes, with cellular details<br>in fetal brains and contains 466 annotated Nissl stained sections, complemented with postmortem<br>magnetic resonance imaging (MRI), block face imaging and more than 4666 histological sections<br>accessible online https://brainportal.humanbrain.in/publicview/index.html. The fetal brain<br>reference atlas has about 500 central nervous system-identified parts.<br>We describe the developing cytoarchitecture and topographical variations from Nissl<br>preparations, sectioned in the sagittal plane (N=4), and the coronal plane (N=1). New findings<br>reveal that the frontal cortex's transitional intermediate zone (IZ) exhibits three subdivisions as<br>early as 21GW. We report the extension of the cell sparse layer between the cortical plate and<br>the subplate originating in the orbital cortex at 14GW and extending to the frontal cortex by 17GW.<br>The occipital and parietal cortices display a characteristic honeycomb pattern of the IZ after 14GW<br>later than previously reported. We describe the development of the thalamic pregeniculate<br>complex and its subdivisions from ventral to dorsal along with the rotation of the lateral geniculate<br>nucleus. High-quality Nissl preparations allowed the identification of several fiber tracts in the<br>thalamus, hypothalamus and pretectal nuclei from 14GW.<br>The current dataset including the 3D reconstruction of the fetal brain has been curated with<br>significant methodological advancements that were enabled by an engineering and computational<br>approach, laying the groundwork for further advancement.

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Axial

Sagittal

Coronal

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Datasets

Brains<br>Age<br>Sectioning Plane<br>Available Datasets<br>Annotations<br>Volumes

Specimen 1<br>25 GW<br>Transverse (Coronal)

Nissl (282)

IHC (39)

78 (sections)

MRI

Histology

Specimen 2<br>9 years<br>Transverse along the longitudinal axis of the...