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.
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.

Copyright: Top left/Middle right: adapted from Schmitz et al., Frontiers (2018); Rest: Schmitz/Schober, Forschungszentrum Jülich GmbH

Selected Publications

Journal Article Henssen, D. J. H. A. (Corresponding author) ; Mollink, J. ; Kurt, E. ; van Dongen, R. ; Bartels, R. H. M. A. ; Gräβel, D. ; Kozicz, T. ; Axer, M. ; Van Cappellen van Walsum, A.-M.
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 (2019) [10.1007/s00429-018-1767-1]2019 Files BibTeX | EndNote: XML, Text | RIS

Contribution to a conference proceedings/Contribution to a book Schmitz, D. ; Amunts, K. ; Lippert, T. ; Axer, M.
A least squares approach for the reconstruction of nerve fiber orientations from tiltable specimen experiments in 3D-PLI
2018
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 (2018) [10.1109/ISBI.2018.8363539]2018 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Schmitz, D. (Corresponding author) ; Münzing, S. ; Schober, M. ; Schubert, N. ; Minnerop, M. ; Lippert, T. ; Amunts, K. ; Axer, M.
Derivation of Fiber Orientations From Oblique Views Through Human Brain Sections in 3D-Polarized Light Imaging
Frontiers in neuroanatomy 12, 75 (2018) [10.3389/fnana.2018.00075]2018 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Poster (Other) Schmitz, D. (Corresponding author) ; Münzing, S. ; Schober, M. ; Schubert, N. ; Schlömer, P. ; Lippert, T. ; Amunts, K. ; Axer, M.
Oblique views through unstained brain sections: a new module to 3D-Polarized Light Imaging
20182018 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

Contribution to a book Halefoğlu, A. M. (Editor) ; Schubert, N. (Corresponding author) ; Axer, M. ; Pietrzyk, U. ; Amunts, K.
3D Polarized Light Imaging Portrayed: Visualization of Fiber Architecture Derived from 3D-PLI
2018High-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 (2018) [10.5772/intechopen.72532]2018 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Contribution to a conference proceedings Sharib, A. (Corresponding author) ; Rohr ; Axer, M. ; Grässel, D. ; Schlömer, P. ; Amunts, K. ; Eils ; Wörz
ELASTIC REGISTRATION OF HIGH-RESOLUTION 3D PLI DATA OF THE HUMAN BRAIN
2017IEEE International Symposium on Biomedical Imaging, ISBI, BarcelonaBarcelona, Spain, 18 Apr 2017 - 21 Apr 20172017-04-182017-04-21 1-5 (2017)2017 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Contribution to a conference proceedings Ali (Corresponding author) ; Rohr ; Axer, M. ; Amunts, K. ; Eils ; Wörz
REGISTRATION OF ULTRA-HIGH RESOLUTION 3D PLI DATA OF HUMAN BRAINSECTIONS TO THEIR CORRESPONDING HIGH-RESOLUTION COUNTERPART
2017IEEE International Symposium on Biomedical Imaging, ISBI, MelbourneMelbourne, Australia, 18 Apr 2017 - 21 Apr 20172017-04-182017-04-21 1-5 (2017)2017 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Contribution to a conference proceedings Hänel (Corresponding author) ; Demiralp ; Axer, M. ; Grässel, D. ; Hentschel ; Kuhlen, T.
Interactive Level-of-Detail Visualization of 3D-Polarized Light Imaging Data Using Spherical Harmonics
2017Eurographics Conference on Visualization, EuroVis, BarcelonaBarcelona, Spain, 12 May 2017 - 16 May 20172017-05-122017-05-16 1-5 (2017)2017 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Contribution to a book Schubert, N. (Corresponding author) ; Grässel, D. ; Pietrzyk, U. ; Amunts, K. ; Axer, M.
Visualization of vector fields derived from 3D Polarized Light Imaging
2016Bildverarbeitung für die Medizin 2016 Heidelberg : Springer, Informatik aktuell 176-181 (2016)2016 BibTeX | EndNote: XML, Text | RIS

Contribution to a conference proceedings Schober, M. (Corresponding author) ; Axer, M. ; Huysegoms, M. ; Schubert, N. ; Amunts, K. ; Dickscheid, T.
Morphing image masks for stacked histological sections using Laplace's equation
2016Bildverarbeitung für die Medizin
BVM-Workshop, BerlinBerlin, Germany, 13 Mar 2016 - 15 Mar 20162016-03-132016-03-15 - (2016)2016 BibTeX | EndNote: XML, Text | RIS

Contribution to a conference proceedings/Contribution to a book Kirlangic, M. E. ; Schubert, N. ; Schober, M. ; Amunts, K. ; Zilles, K. ; Axer, M.
Reconstructing a Series of Auto-Radiographic Images in Rat Brains
2015Bildverarbeitung 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 (2015) [10.1007/978-3-662-46224-9_30]2015 BibTeX | EndNote: XML, Text | RIS

Contribution to a conference proceedings/Contribution to a book Schubert, N. ; Kirlangic, M. E. ; Schober, M. ; Huynh, A. M. ; Amunts, K. ; Zilles, K. ; Axer, M.
3D Reconstruction of Histological Rat Brain Images
2015Bildverarbeitung 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 (2015) [10.1007/978-3-662-46224-9_27]2015 BibTeX | EndNote: XML, Text | RIS

Contribution to a conference proceedings/Contribution to a book Schober, M. ; Schlömer, P. ; Cremer, M. ; Mohlberg, H. ; Huynh, A. M. ; Schubert, N. ; Kirlangic, M. E. ; Amunts, K.
Reference Volume Generation for Subsequent 3D Reconstruction of Histological Sections
2015Bildverarbeitung 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 (2015) [10.1007/978-3-662-46224-9_26]2015 BibTeX | EndNote: XML, Text | RIS