Navigation and service


3D Polarized Light Imaging (PLI)

3D Polarized Light Imaging (PLI) enables the mapping of single nerve fibers in postmortem human brains in unprecedented detail. Due to the very high resolution at sub-millimeter scale, an immense amount of image data has to be reconstructed three-dimensionally before it can be analyzed.

For data acquisition, the brain is sectioned in slices of a thickness of 70µm. The slices are mounted on specimen slides. Measurements are performed using the large area polarimeter, or the polarizing microscope, or both. This results in a multi-modal data set. The resolution of the data varies from 64 x 64 (µm)2 to 1.6 x 1.6 (µm)2 inplane, depending on the measuring instrument.

The reconstruction consists of a post-processing after capturing the data including stitching and segmentation. A registration is performed with respect to reference images of the cut brain. Finally, the fibre orientation map is synthesized from the measured data yielding complex information about the course of nerve fibres.

Picture at the right: Overlapping of raw data and segmentation masks.

PLI – Our Contribution

  • Methodological

    • Statistical data analysis
    • Image segmentation on a GPU cluster
    • Pre-processing tools for file format integration and data manipulation
    • Automated quality checks of the PLI workflow
  • Software development

    • Guidance on HPC usage and parallel programming paradigms MPI and CUDA
    • Assistance in efficiently joining C/C++ and Python in neuroscientific software

Selected references

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings/Contribution to a book
Hybrid parallelization of a seeded region growing segmentation of brain images for a GPU cluster
ARCS 2014: 27th International Conference on Architecture of Computing Systems - Workshop Proceedings
27th International Conference on Architecture of Computing Systems, ARCS2014, LübeckLübeck, Germany, 25 Feb 2014 - 28 Feb 20142014-02-252014-02-28
Berlin : VDE Verlag 190 pp. () OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article  ;  ;  ;  ;
Relating Polarized Light Imaging Data Across Scales
Imaging the brain at different scales: How to integrate multi-scale structural information?, AntwerpAntwerp, Belgium, 2 Sep 2013 - 6 Sep 20132013-09-022013-09-06 Frontiers in neuroinformatics 7, 3 () [10.3389/conf.fninf.2013.10.00029] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS


Servicemeu

Homepage