DOI: 10.5281/zenodo.17431227
title: Ex-vivo dataset for validation of MRI-based axon radius mapping

description: Overview

The dataset provides histological axon radius distributions and ex-vivo dMRI data used in "MRI-scale histology validates spatial sensitivity of in-vivo MRI-based axon radius estimation" (Imaging Neuroscience, 2025,  https://doi.org/10.1162/IMAG.a.1030). The dataset includes axon radius distributions of two human corpus callosum tissue samples scanned with histology (light microscopy); one of the samples was also scanned with ex-vivo diffusion MRI.

Histology

Axon radius distributions from light microscopy data acquired at 0.1112 µm/pixel resolution with 40× objective (NA 0.95). Semi-thin sections (~500 nm thickness) were stained with 1% toluidine blue.

Key files:



`roiinfo.tsv`: ROI spatial information and area measurements

`desc-countsCircularEq_radii.tsv`: Axon radius distributions (circular equivalent)

`desc-binCenters_radii.tsv` and `desc-binEdges_radii.tsv`: Histogram bin information

`desc-polygons_roicoords.tsv`: ROI polygon coordinates


Ex Vivo MRI

Diffusion-weighted MRI acquired on a Bruker 9.4T scanner with maximum gradient amplitude of 1500 mT/m. Data includes:



b-values: 2.5 to 100 ms/µm²

65 gradient directions per b-value

Isotropic voxel size: 0.35 mm

TE = 34.7 ms, δ = 7 ms, Δ = 20.1 ms


**Only available for subject ev-01** (CC-01 hemisphere not used for histology).

ROI Naming

Histology ROIs are named by anatomical region (e.g., AM1, G2, M3, PM1, S6):



AM = Anterior Midbody

G = Genu

M = Midbody

PM = Posterior Midbody

S = Splenium


References

Mordhorst, L., Edwards, L.J., Morozova, M., Ashtarayeh, M., Streubel, T., Fricke, B., Fritz, F.J., Rusch, H., Jäger, C., Starke, L., Gladytz, T., Tasbihi, E., Periquito, J.S., Pohlmann, A., Mushumba, H., Püschel, K., Niendorf, T., Weiskopf, N., Morawski, M., & Mohammadi, S. (2025). MRI-scale histology validates spatial sensitivity of in-vivo MRI-based axon radius estimation. Imaging Neuroscience, Advance Publication. https://doi.org/10.1162/IMAG.a.1030

Mordhorst L, Morozova M, Papazoglou S, Fricke B, Oeschger JM, Tabarin T, Rusch H, Jäger C, Geyer S, Weiskopf N, Morawski M, Mohammadi S. Towards a representative reference for MRI-based human axon radius assessment using light microscopy. Neuroimage. 2022 Apr 1;249:118906. doi: 10.1016/j.neuroimage.2022.118906. Epub 2022 Jan 13. PMID: 35032659. https://doi.org/10.1016/j.neuroimage.2022.118906

Acknowledgements

The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-­2013) / ERC grant agreement number 616905. This work was supported by the German Research Foundation (DFG Priority Program 2041 “Computational Connectomics”, [MO 2397/5-­ 1, MO 2397/5-­2, MO 2249/3-­1, MO 2249/3-­2], by the Emmy Noether Stipend: MO 2397/4-­1; MO 2397/4-­2). Funded by the European Union. Views and opinionsexpressed are, however, those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them. This work is supported by ERC grant (Acronym: MRStain, Grant agreement ID: 101089218, DOI: 10.3030/101089218). Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – project no. 347592254 (WE 5046/4-2).