Synopsis: A new open-access platform at anchor.humanbrain.in provides a readily available online histological and neurochemical mapping of the human brainstem at three stages: 25 fetal gestational weeks (GW), 9 years old, and 54 years old.
The brainstem remains one of the most challenging regions for both surgical intervention and pathological correlation. CT imaging is generally poor, and MRI imaging often lacks cues to decide upon functional zones. The new atlas allows histochemical and MRI images to be evaluated side by side.
According to the preprint at biorxiv, this online atlas was constructed from three whole-brain specimens representing distinct developmental stages:
| Fetus at 25 gestational weeks (critical window for brainstem nuclei maturation) |
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| Child at 9 years (most development completed, still some myelinating) |
| 54 years (adult, representative of mature, aging brainstem) |
More than 800 serial sections were processed using both the usual Nissl staining for cytoarchitectonic demarcation as well as 7 different immunochemical (IHC) markers enabling neurochemical characterization of specific cell populations, including catecholaminergic groups (dopaminergic, noradrenergic, and adrenergic nuclei). I inspected the catachlamine staining of the substantia nigra compacta and found it clear and well labeled. In fact, I found the anatomic labeling applied to the sections to be quite impressively thorough. Over 200 structures are stated to be manually annotated across all three specimens. Even the within-brain cranial nerve pathways seem clearly delineated and annotated. Highly recommended, though it needs a better index.
ABSTRACT
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ANCHOR : Atlas of Neurochemical Characterization of the Human Brainstem with 3D Reconstruction
Authors: Mihail Bota, Soundharya Venkatesh, Shevani Arun Arunesh, Nagajothi Ganesan, Supriti Mulay, Karan Ramana Gopi, Sruti Rekha Muni, Shrimathi Mani, Sam C. Chrisline, A.S.T. Aditya Bharg, Kanna G Vinoth, 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
doi: https://doi.org/10.64898/2026.06.03.727794
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 https://anchor.humanbrain.in/.
