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. 2019 Dec 3;13:75. doi: 10.3389/fninf.2019.00075

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Copyright © 2019 Yates, Groeneboom, Coello, Lichtenthaler, Kuhn, Demuth, Hartlage-Rübsamen, Roßner, Leergaard, Kreshuk, Puchades and Bjaalie.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Workflow for automated quantification and spatial analysis. Diagram showing key steps of the workflow (blue frames). After sectioning and labelling, brain sections are digitalised. Serial section images are pre-processed, and then registered to a 3-D reference atlas space using the QuickNII tool. The same images are segmented using the ilastik tool. Exported custom atlas maps and segmented images are then combined in the Nutil tool in order to extract quantification of objects in atlas brain regions as well as 3D coordinates of the objects.