A neuroimaging atlas of the nigrosomes in the substantia nigra based on 3D histology.

Overview

1. Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences,Stephanstr. 1a, 04103 Leipzig, Germany
2. Microstructure Mapping Lab, University Hospital Lausanne,Rue du Bugnon 46, 1011 Lausanne, Switzerland
3. Integrative Model-based Cognitive Neuroscience Research Unit, University of Amsterdam,Amsterdam, Nieuwe Achtergracht 129B, 1001 NK Amsterdam, The Netherlands
4. Full Brain Picture Analytics, Lage Morsweg 73, 2332 XB Leiden, The Netherlands
5. Felix Bloch Institute for Solid State Physics, Faculty of Physics and Earth System Sciences, Leipzig University,Linnéstraße 5, 04103 Leipzig, Germany
6. Paul Flechsig Institute - Centre of Neuropathology and Brain Research, Medical Faculty, Leipzig University,Liebigstraße 19, 04103 Leipzig, Germany
7. Sleep and Health Lab, GIGA-Institute, CRC-Human Imaging Unit, University of Liége (ULiége),Allée du Six Août, 8 (B30), 4000 Sart Tilman Liége, Belgium
8. Department of Anatomy and Embryology, Maastricht University,Universiteitssingel 50, 6229 HA Maastricht, Netherlands
9. C. & O. Vogt Institute for Brain Research, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf,Merowingerplatz 1A, 0225 Düsseldorf, Germany
10. Forschungszentrum Jülich, INM-1,52425 Jülich, Germany
11. Wellcome Centre for Human Neuroimaging, Institute of Neurology, University College London,12 Queen Square, London, WC1N 3AR UK

Abstract

Nigrosomes are formed by clusters of pigmented dopaminergic cells in the substantia nigra that critically contribute to dopaminergic function. The ever-increasing resolution of ultra-high-field MRI brings clinical imaging of these clusters into reach, promising unprecedented insight into the functional role of the nigrosomes and their early degeneration in Parkinson’s disease. However, due to the nigrosomes’ small extents and intricate shapes, they are not included in current MRI brain atlases, preventing nigrosome-specific MRI data analysis. We provide a comprehensive 3D histological atlas of the five nigrosomes co-aligned to the widely-used MNI152 2009b space. This atlas is based on 3D-reconstructed, ultra-high-resolution block-face images and gold-standard nigrosome delineations in calbindin-D28K immunohistochemistry. We validated the atlas’s accuracy using the multimodal ultra-high-resolution post mortem BigBrain dataset and demonstrated its consistency with qualitative nigrosome atlases based on classical 2D histology. We provide detailed usage instructions for applying our atlas to ultra-high-resolution and -field MRI data. The openly available atlas enables neuroimaging studies of the nigrosomes, opening a new avenue toward understanding the differential involvement of the nigrosomes in the healthy and diseased brain and the development of neuroimaging biomarkers of dopaminergic neurodegeneration.

Reproduced under the paper's license (CC BY), from the paper cited above.

Code

The paper links to its data, not to its authors' code: see the Data section.

Code availability

Code for aligning and generating the nigrosome atlas is available in the data repository as Jupyter notebooks45. As a use case, we applied the nigrosome atlas to an in vivo quantitative MRI dataset using the provided registration script (Fig. 7).

Reproduced under the paper's license (CC BY), from the paper cited above.

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Data

Datasets cited

• osf:gsphy, at OSF; found in the text, “Registration of nigrosome probability maps to…”

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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 17 authors, 6 MeSH terms, 2 funders, 46 references.

Cite

This paper

Brammerloh, M., Alkemade, A., Bazin, P.-L., Jantzen, C., Jäger, C., Gasparello, A., Zubkov, M., Talwar, P., Vandewalle, G., Herrler, A., Pine, K. J., Morawski, M., Balesar, R., Amunts, K., Forstmann, B. U., Weiskopf, N., & Kirilina, E. (2026). A neuroimaging atlas of the nigrosomes in the substantia nigra based on 3D histology. Scientific data, 13(1), 1255. https://doi.org/10.1038/s41597-026-08133-y

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