Journal Article

FZJ-2022-01891

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Automated computation of nerve fibre inclinations from 3D polarised light imaging measurements of brain tissue

Menzel, M. (Corresponding author)FZJ* ; Reuter, J. A.FZJ* ; Gräßel, D.FZJ* ; Costantini, I. ; Amunts, K.FZJ* ; Axer, M.FZJ*

2022
Macmillan Publishers Limited, part of Springer Nature [London]

This record in other databases:    

Please use a persistent id in citations: http://hdl.handle.net/2128/31061  doi:10.1038/s41598-022-08140-0

Abstract: The method 3D polarised light imaging (3D-PLI) measures the birefringence of histological brain sections to determine the spatial course of nerve fibres (myelinated axons). While the in-plane fibre directions can be determined with high accuracy, the computation of the out-of-plane fibre inclinations is more challenging because they are derived from the amplitude of the birefringence signals, which depends e.g. on the amount of nerve fibres. One possibility to improve the accuracy is to consider the average transmitted light intensity (transmittance weighting). The current procedure requires effortful manual adjustment of parameters and anatomical knowledge. Here, we introduce an automated, optimised computation of the fibre inclinations, allowing for a much faster, reproducible determination of fibre orientations in 3D-PLI. Depending on the degree of myelination, the algorithm uses different models (transmittance-weighted, unweighted, or a linear combination), allowing to account for regionally specific behaviour. As the algorithm is parallelised and GPU optimised, it can be applied to large data sets. Moreover, it only uses images from standard 3D-PLI measurements without tilting, and can therefore be applied to existing data sets from previous measurements. The functionality is demonstrated on unstained coronal and sagittal histological sections of vervet monkey and rat brains.

---

Contributing Institute(s):

1. Strukturelle und funktionelle Organisation des Gehirns (INM-1)

Research Program(s):

1. 5254 - Neuroscientific Data Analytics and AI (POF4-525) (POF4-525)
2. HBP SGA3 - Human Brain Project Specific Grant Agreement 3 (945539) (945539)
3. JL SMHB - Joint Lab Supercomputing and Modeling for the Human Brain (JL SMHB-2021-2027) (JL SMHB-2021-2027)

Appears in the scientific report 2022

---

Database coverage:
; ; ; ; Article Processing Charges ; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; Current Contents - Physical, Chemical and Earth Sciences ; DOAJ Seal ; Ebsco Academic Search ; Essential Science Indicators ; Fees ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection ; Zoological Record

---