Do it yourself: Creating 3D brain-surface models and custom-made brain matrices for guided sectioning using photogrammetry and three-dimensional printing technology

Holtz, S.; Hechavarria, J. C.; Knörnschild, M.; Scharff, C.

doi:10.1101/2025.01.27.635028

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bioRxiv · 10.1101/2025.01.27.635028

Do it yourself: Creating 3D brain-surface models and custom-made brain matrices for guided sectioning using photogrammetry and three-dimensional printing technology

Holtz, S.·Hechavarria, J. C.·Knörnschild, M.·Scharff, C.

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Abstract

Neuroethologists study many non-model animals. The development of techniques for precise and standardized histological brain analysis is key for understanding neural mechanisms across species. Here we present a novel cost-effective approach combining photogrammetry and three-dimensional printing technology to generate 3D brain surface models and produce species-specific brain matrices for precise and reproducible trimming, blocking, and sectioning of brain tissue. Using this strategy, we generated the first 3D brain surface model and brain matrix for Sebas short-tailed fruit bat Carollia perspicillata, CP. We generated the 3D brain surface model with the open-source 3D graphics suite Blender and its inexpensive photogrammetry plug-in Snapmesh. High-quality photographs of two male CP brains were used for the 3D-reconstruction, resulting in a 3D surface model. Photogrammetry thus offers a viable, cheap alternative to techniques otherwise requiring access to costly 3D- or CT-scanners. The brain matrix was then modeled using Blender, and printed using a 3D printer. Our brain matrix facilitates and standardizes trimming or blocking of brains, providing consistent access to brain regions of CP in the sagittal and coronal planes. Using this workflow, brain surface models and brain matrices can be produced from brains without tissue loss. Our approach provides an affordable, and tissue-preserving alternative for the generation of 3D brain surface models and brain matrices and will benefit researchers globally, especially those with limited funding, no access to scanners or working with particularly valuable specimen.

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Holtz, S., Hechavarria, J. C., Knörnschild, M., Scharff, C.. 2025-01-28. Do it yourself: Creating 3D brain-surface models and custom-made brain matrices for guided sectioning using photogrammetry and three-dimensional printing technology. https://doi.org/10.1101/2025.01.27.635028

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