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. 2023 Jun 29;21(6):e3002158. doi: 10.1371/journal.pbio.3002158

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© 2023 Skibbe et al

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Fig 2 — The steps of the BMCR image post-processing pipeline: (a) Image acquisition: After dMRI imaging and automated STPT imaging and sectioning using 2p-tomography, retrograde tracer, Nissl and backlit images are taken. (b) Processing and analysis of anterograde imaging data, and (c) retrograde imaging data, respectively. (d) Automated alignment of Nissl and backlit images. (e) Track-density images are generated from streamlines representing major axon fiber bundles touching the injection site. (f) All data, including high-resolution microscopy data are mapped to the BMCR 3D brain reference image space. The final steps (g) are creating the flatmap stack, (h) preparing the data for downloading, and (i) integrating it into the BMCR-Explorer. BMCR, Brain/MINDS Marmoset Connectivity Resource; dMRI, diffusion-weighted MRI; STPT, serial two-photon tomography.