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Convolutional neural networks for cytoarchitectonic brain mapping at large scale.
Neuroimage 240:118327 (2021)
Publ. Version/Full Text
Research data
DOI
PMC
Human brain atlases provide spatial reference systems for data characterizing brain organization at different levels, coming from different brains. Cytoarchitecture is a basic principle of the microstructural organization of the brain, as regional differences in the arrangement and composition of neuronal cells are indicators of changes in connectivity and function. Automated scanning procedures and observer-independent methods are prerequisites to reliably identify cytoarchitectonic areas, and to achieve reproducible models of brain segregation. Time becomes a key factor when moving from the analysis of single regions of interest towards high-throughput scanning of large series of whole-brain sections. Here we present a new workflow for mapping cytoarchitectonic areas in large series of cell-body stained histological sections of human postmortem brains. It is based on a Deep Convolutional Neural Network (CNN), which is trained on a pair of section images with annotations, with a large number of un-annotated sections in between. The model learns to create all missing annotations in between with high accuracy, and faster than our previous workflow based on observer-independent mapping. The new workflow does not require preceding 3D-reconstruction of sections, and is robust against histological artefacts. It processes large data sets with sizes in the order of multiple Terabytes efficiently. The workflow was integrated into a web interface, to allow access without expertise in deep learning and batch computing. Applying deep neural networks for cytoarchitectonic mapping opens new perspectives to enable high-resolution models of brain areas, introducing CNNs to identify borders of brain areas.
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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
Brain Mapping ; Cortex ; Cytoarchitecture ; Deep Learning ; Histology ; Human Brain ; Segmentation; Cerebral-cortex; Region; Atlas
ISSN (print) / ISBN
1053-8119
e-ISSN
1095-9572
Quellenangaben
Volume: 240,
Article Number: 118327
Publisher
Elsevier
Publishing Place
525 B St, Ste 1900, San Diego, Ca 92101-4495 Usa
Non-patent literature
Publications
Reviewing status
Peer reviewed
Institute(s)
Institute of Computational Biology (ICB)
Helmholtz AI - FZJ (HAI - FZJ)
Helmholtz AI - FZJ (HAI - FZJ)
Grants
Max Planck Society for the Advancement of Science
German Federal Ministry of Education and Research (BMBF)
German Research Foundation (DFG)
Helmholtz Association's Initiative and Networking Fund through the Helmholtz International BigBrain Analytics and Learning Laboratory (HIBALL) under the Helmholtz International Lab
European Union's Horizon 2020 research and innovation programme
German Federal Ministry of Education and Research (BMBF)
German Research Foundation (DFG)
Helmholtz Association's Initiative and Networking Fund through the Helmholtz International BigBrain Analytics and Learning Laboratory (HIBALL) under the Helmholtz International Lab
European Union's Horizon 2020 research and innovation programme