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A scalable multimodal approach for quantifying the nerve fiber architecture of the human brain / vorgelegt von Kai Benning. Wuppertal, Mai 2024
Inhalt
Introduction
I Basics
The human brain in a Nutshell
From brain preparation to 3D Polarized Light Imaging
Polarized light microscopy
Large Area Polarimeter (LAP)
Large Metripol Polarimeter 3D (LMP-3D)
Directional Analysis of 3D Polarized Light Imaging
Established 3D-PLI analysis
Calibration
Fourier Analysis
Least Squares Fitting
II 3D Polarized Light Imaging meets High-Performance Computing
Towards an automatic workflow on HPC
Data and Metadata
Software Testing
Introduction
Development
Results
Discussion
The Minimal Working Workflow
Introduction
Development
Results
Discussion
Workflow Update 1: Parallelizing the Directional Analysis
Introduction
Methods
Results
Discussion
Workflow Update 2: Automatic noise and artifact removal
Introduction
Methods
Results
Discussion
III Estimating uncertainties
Calculating uncertainties of fiber orientations
Probabilities of Orientations in 3D-PLI
Monte-Carlo Markow-Chain (MCMC) for 3D-PLI
Accelerating the uncertainty analysis with GPUs
Introduction
Methods
Results
Discussion
Learning and visualizing uncertainties
Introduction
Methods
Results
Discussion
IV Bridging Modalities and Scales
Bridging Modalities and Scales
Introduction
Material and Methods
Interactive Preregistration
Registration and Reorientation
Volume creation
3D-Registration and Correlative Analysis
Results
Discussion
V Overarching Discussion
Conclusion and Outlook
Tissue Preparation and Sectioning
Amsterdam Brain
Düsseldorf Brain
Chenonceau Brain
3D-PLI Systems
Mathematica notebook
JURECA DC