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Signal and Image Processing

To reconstruct the nerve fiber architecture from the images generated in the 3D-PLI measurement, various methods of signal and image processing are employed. The methods are validated by analytical methods and numerical simulations.

HPC infrastructure for processing large image data

To process and handle the measurement data of up to 1 Terabyte per brain section, the resources of the Jülich Supercomputing Centre (JSC) are exploited. The developed software utilizes either a large number of processors or graphic cards.

Computational Workflow: This workflow describes the different steps, computing platform and output images of the 3D-PLI workflow.Computational Workflow: This workflow describes the different steps, computing platform and output images of the 3D-PLI workflow.
Copyright: Forschungszentrum Jülich GmbH

Methods of Signal and Image Processing

The parameter maps shown in the figure above (transmittance, direction, retardation, inclination) are extracted from the measured raw images by employing different methods of signal and image processing.

Methods of Signal and Image ProcessingCopyright: Top left/Middle right: adapted from Schmitz et al., Frontiers (2018); Rest: Schmitz/Schober, Forschungszentrum Jülich GmbH

Selected Publications

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Ex vivo visualization of the trigeminal pathways in the human brainstem using 11.7T diffusion MRI combined with microscopy polarized light imaging
Brain structure & function 224(1), 159-170 () [10.1007/s00429-018-1767-1]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings/Contribution to a book
A least squares approach for the reconstruction of nerve fiber orientations from tiltable specimen experiments in 3D-PLI

2018 IEEE 15th International Symposium on Biomedical Imaging, ISBI 2018, WashingtonWashington, DC, 4 Apr 2018 - 7 Apr 20182018-04-042018-04-07
[Piscataway, NJ] : IEEE 132 - 135 () [10.1109/ISBI.2018.8363539] 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
Derivation of Fiber Orientations From Oblique Views Through Human Brain Sections in 3D-Polarized Light Imaging
Frontiers in neuroanatomy 12, 75 () [10.3389/fnana.2018.00075] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Oblique views through unstained brain sections: a new module to 3D-Polarized Light Imaging
2018 Annual Meeting of the Organization of Human Brain Mapping (OHBM), SingaporeSingapore, Singapore, 18 Jun 2018 - 21 Jun 20182018-06-182018-06-21 BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a book
3D Polarized Light Imaging Portrayed: Visualization of Fiber Architecture Derived from 3D-PLI
High-Resolution Neuroimaging - Basic Physical Principles and Clinical Applications / Halefoğlu, Ahmet Mesrur (Editor) ; : InTech, , Chapter 3 ; ISBN: 978-953-51-3865-5 ; doi:10.5772/intechopen.68268 - : InTech 29-46 () [10.5772/intechopen.72532] 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 Contribution to a conference proceedings
ELASTIC REGISTRATION OF HIGH-RESOLUTION 3D PLI DATA OF THE HUMAN BRAIN
IEEE International Symposium on Biomedical Imaging, ISBI, BarcelonaBarcelona, Spain, 18 Apr 2017 - 21 Apr 20172017-04-182017-04-21 1-5 () 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 Contribution to a conference proceedings
REGISTRATION OF ULTRA-HIGH RESOLUTION 3D PLI DATA OF HUMAN BRAINSECTIONS TO THEIR CORRESPONDING HIGH-RESOLUTION COUNTERPART
IEEE International Symposium on Biomedical Imaging, ISBI, MelbourneMelbourne, Australia, 18 Apr 2017 - 21 Apr 20172017-04-182017-04-21 1-5 () 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 Contribution to a conference proceedings
Interactive Level-of-Detail Visualization of 3D-Polarized Light Imaging Data Using Spherical Harmonics
Eurographics Conference on Visualization, EuroVis, BarcelonaBarcelona, Spain, 12 May 2017 - 16 May 20172017-05-122017-05-16 1-5 () 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 Contribution to a book
Visualization of vector fields derived from 3D Polarized Light Imaging
Bildverarbeitung für die Medizin 2016 Heidelberg : Springer, Informatik aktuell 176-181 () BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings
Morphing image masks for stacked histological sections using Laplace's equation
Bildverarbeitung für die Medizin
BVM-Workshop, BerlinBerlin, Germany, 13 Mar 2016 - 15 Mar 20162016-03-132016-03-15
- () BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings/Contribution to a book
Reconstructing a Series of Auto-Radiographic Images in Rat Brains
Bildverarbeitung für die Medizin 2015 / Handels, Heinz (Editor) ; Berlin, Heidelberg : Springer Berlin Heidelberg, 2015, Chapter 30 ; ISSN: 1431-472X ; ISBN: 978-3-662-46223-2=978-3-662-46224-9 ; doi:10.1007/978-3-662-46224-9
Workshop Bildverarbeitung für die Medizin 2015, LübeckLübeck, Germany, 15 Mar 2015 - 17 Mar 20152015-03-152015-03-17
Berlin, Heidelberg : Springer Berlin Heidelberg, Informatik aktuell 167 - 172 () [10.1007/978-3-662-46224-9_30] BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings/Contribution to a book
3D Reconstruction of Histological Rat Brain Images
Bildverarbeitung für die Medizin 2015 / Handels, Heinz (Editor) ; Berlin, Heidelberg : Springer Berlin Heidelberg, 2015, Chapter 27 ; ISSN: 1431-472X ; ISBN: 978-3-662-46223-2=978-3-662-46224-9 ; doi:10.1007/978-3-662-46224-9
Workshop Bildverarbeitung für die Medizin 2015, LübeckLübeck, Germany, 15 Mar 2015 - 17 Mar 20152015-03-152015-03-17
Berlin, Heidelberg : Springer Berlin Heidelberg, Informatik aktuell 149 - 154 () [10.1007/978-3-662-46224-9_27] BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings/Contribution to a book
Reference Volume Generation for Subsequent 3D Reconstruction of Histological Sections
Bildverarbeitung für die Medizin 2015 / Handels, Heinz (Editor) ; Berlin, Heidelberg : Springer Berlin Heidelberg, 2015, Chapter 26 ; ISSN: 1431-472X ; ISBN: 978-3-662-46223-2=978-3-662-46224-9 ; doi:10.1007/978-3-662-46224-9
Workshop Bildverarbeitung für die Medizin 2015, LübeckLübeck, Germany, 15 Mar 2015 - 17 Mar 20152015-03-152015-03-17
Berlin, Heidelberg : Springer Berlin Heidelberg, Informatik aktuell 143 - 148 () [10.1007/978-3-662-46224-9_26] BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a book
Optimized Signal Separation for 3D-Polarized Light Imaging
Functional Brain Mapping and the Endeavor to Understand the Working Brain Rijeka, Croatia : InTech 355-374 () [10.5772/55246]  Download fulltext Files  Download fulltextFulltext BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Signal enhancement in polarized light imaging by means of independent component analysis
NeuroImage 49, 1241 - 1248 () [10.1016/j.neuroimage.2009.08.059] BibTeX | EndNote: XML, Text | RIS

Additional Information

PLI Logo

Groupleader

Dr. rer. nat. Markus Axer

Building: 15.9, Room: 3029

Institute of Neuroscience and Medicine (INM-1)
Forschungszentrum Jülich
52425 Jülich

Tel.: +49 2461 61-6314
Fax: +49 2461 61-2820
E-Mail: m.axer@fz-juelich.de

Management

Stefanie Hennen

Building: 15.9, Room: 3021

+49 2461 61-2481
 +49-2461 61-3483
s.hennen@fz-juelich.de

Janine Hucko

Building: 15.9, Room: 3020

+49 2461 61-6443
+49 2461 61-3483
j.hucko@fz-juelich.de

Address

Institut für Neurowissenschaften und Medizin (INM-1)
Forschungszentrum Jülich
52425 Jülich

Building: 15.9


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