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1

EduGATE – basic examples for educative purpose using the GATE simulation platform

Pietrzyk, Uwe, Zakhnini, Abdelhamid, Axer, Markus, Sauerzapf, Sophie, Benoit, Didier, Gaens, Michaela

Journal:

Zeitschrift für Medizinische Physik

Year:

2013

Language:

english

File:

PDF, 1002 KB

english, 2013

2

Nerve Ultrasound Predicts Treatment Response in Chronic Inflammatory Demyelinating Polyradiculoneuropathy—a Prospective Follow-Up

Härtig, Florian, Ross, Marlene, Dammeier, Nele Maria, Fedtke, Nadin, Heiling, Bianka, Axer, Hubertus, Décard, Bernhard F., Auffenberg, Eva, Koch, Marilin, Rattay, Tim W., Krumbholz, Markus, Bornemann,

Journal:

Neurotherapeutics

Year:

2018

Language:

english

File:

PDF, 2.04 MB

english, 2018

3

Rigid and non-rigid registration of polarized light imaging data for 3D reconstruction of the temporal lobe of the human brain at micrometer resolution

Ali, Sharib, Wörz, Stefan, Amunts, Katrin, Eils, Roland, Axer, Markus, Rohr, Karl

Journal:

Year:

2018

File:

PDF, 6.69 MB

2018

4

Rigid and non-rigid registration of polarized light imaging data for 3D reconstruction of the temporal lobe of the human brain at micrometer resolution

Ali, Sharib, Wörz, Stefan, Amunts, Katrin, Eils, Roland, Axer, Markus, Rohr, Karl

Journal:

Year:

2018

Language:

english

File:

PDF, 6.69 MB

english, 2018

5

Ex vivo visualization of the trigeminal pathways in the human brainstem using 11.7T diffusion MRI combined with microscopy polarized light imaging

Henssen, Dylan J. H. A., Mollink, Jeroen, Kurt, Erkan, van Dongen, Robert, Bartels, Ronald H. M. A., Gräβel, David, Kozicz, Tamas, Axer, Markus, Van Cappellen van Walsum, Anne-Marie

Journal:

Brain Structure and Function (Anatomy and Embryology 1891-2006)

Year:

2018

Language:

english

File:

PDF, 2.26 MB

english, 2018

6

The hippocampus of birds in a view of evolutionary connectomics

Herold, Christina, Schlömer, Philipp, Mafoppa-Fomat, Isabelle, Mehlhorn, Julia, Amunts, Katrin, Axer, Markus

Journal:

Year:

2018

Language:

english

File:

PDF, 6.31 MB

english, 2018

7

MEDUSA: A GPU-based tool to create realistic phantoms of the brain microstructure using tiny spheres

Ginsburger, Kévin, Matuschke, Felix, Poupon, Fabrice, Mangin, Jean-François, Axer, Markus, Poupon, Cyril

Journal:

Year:

2019

File:

PDF, 45.42 MB

2019

8

Toward a High-Resolution Reconstruction of 3D Nerve Fiber Architectures and Crossings in the Brain Using Light Scattering Measurements and Finite-Difference Time-Domain Simulations

Menzel, Miriam, Axer, Markus, De Raedt, Hans, Costantini, Irene, Silvestri, Ludovico, Pavone, Francesco S., Amunts, Katrin, Michielsen, Kristel

Journal:

Physical Review X

Year:

2020

File:

PDF, 7.52 MB

2020

9

Quantitative estimation of 3-D fiber course in gross histological sections of the human brain using polarized light

Hubertus Axer, Markus Axer, Timo Krings, Diedrich Graf v. Keyserlingk

Journal:

Journal of Neuroscience Methods

Year:

2001

Language:

english

File:

PDF, 1.21 MB

english, 2001

10

Signal enhancement in polarized light imaging by means of independent component analysis

Jürgen Dammers, Markus Axer, David Gräßel, Christoph Palm, Karl Zilles, Katrin Amunts, Uwe Pietrzyk

Journal:

Year:

2010

Language:

english

File:

PDF, 521 KB

english, 2010

11

A novel approach to the human connectome: Ultra-high resolution mapping of fiber tracts in the brain

Markus Axer, Katrin Amunts, David Grässel, Christoph Palm, Jürgen Dammers, Hubertus Axer, Uwe Pietrzyk, Karl Zilles

Journal:

Year:

2011

Language:

english

File:

PDF, 2.52 MB

english, 2011

12

Automatic identification of gray and white matter components in polarized light imaging

Jürgen Dammers, Lukas Breuer, Markus Axer, Melanie Kleiner, Björn Eiben, David Gräßel, Timo Dickscheid, Karl Zilles, Katrin Amunts, N. Joni Shah, Uwe Pietrzyk

Journal:

Year:

2012

Language:

english

File:

PDF, 2.98 MB

english, 2012

13

A new constrained ICA approach for optimal signal decomposition in polarized light imaging

Breuer, Lukas, Axer, Markus, Dammers, Jürgen

Journal:

Journal of Neuroscience Methods

Year:

2013

Language:

english

File:

PDF, 3.05 MB

english, 2013

14

[IEEE 2007 IEEE Nuclear Science Symposium Conference Record - Honolulu, HI, USA (2007.10.26-2007.11.3)] 2007 IEEE Nuclear Science Symposium Conference Record - Nerve fiber mapping of the human visual cortex using Polarized Light Imaging (PLI)

Axer, Markus, Axer, Hubertus, Grassel, David, Amunts, Katrin, Zilles, Karl, Pietrzyk, Uwe

Year:

2007

Language:

english

File:

PDF, 174 KB

english, 2007

15

Understanding fiber mixture by simulation in 3D Polarized Light Imaging

Dohmen, Melanie, Menzel, Miriam, Wiese, Hendrik, Reckfort, Julia, Hanke, Frederike, Pietrzyk, Uwe, Zilles, Karl, Amunts, Katrin, Axer, Markus

Journal:

Year:

2015

Language:

english

File:

PDF, 3.00 MB

english, 2015

16

Target sites for transcallosal fibers in human visual cortex – A combined diffusion and polarized light imaging study

Caspers, Svenja, Axer, Markus, Caspers, Julian, Jockwitz, Christiane, Jütten, Kerstin, Reckfort, Julia, Grässel, David, Amunts, Katrin, Zilles, Karl

Journal:

Year:

2015

Language:

english

File:

PDF, 4.75 MB

english, 2015

17

SPIE Proceedings [SPIE SPIE Sensing Technology + Applications - Baltimore, Maryland, USA (Monday 5 May 2014)] Polarization: Measurement, Analysis, and Remote Sensing XI - Polarized light imaging of the human brain: a new approach to the data analysis of tilted sections

Chenault, David B., Goldstein, Dennis H., Wiese, Hendrik, Gräßel, David, Pietrzyk, Uwe, Amunts, Katrin, Axer, Markus

Year:

2014

Language:

english

File:

PDF, 2.21 MB

english, 2014

18

[OSA Optics and the Brain - Vancouver (2015..-..)] Optics in the Life Sciences - Towards a High-resolution Fiber Model of the Human Brain with 3D Polarized Light Imaging

Axer, Markus, Grässel, David, Amunts, Katrin

Year:

2015

Language:

english

File:

PDF, 1.82 MB

english, 2015

19

[OSA Bio-Optics: Design and Application - Vancouver (2015..-..)] Optics in the Life Sciences - Simulation-Based Validation of the Physical Model in 3D Polarized Light Imaging

Menzel, Miriam, Dohmen, Melanie, De Raedt, Hans, Michielsen, Kristel, Amunts, Katrin, Axer, Markus

Year:

2015

Language:

english

File:

PDF, 420 KB

english, 2015

20

Direct Visualization and Mapping of the Spatial Course of Fiber Tracts at Microscopic Resolution in the Human Hippocampus

Zeineh, Michael M., Palomero-Gallagher, Nicola, Axer, Markus, Gräβel, David, Goubran, Maged, Wree, Andreas, Woods, Roger, Amunts, Katrin, Zilles, Karl

Journal:

Cerebral Cortex

Year:

2016

Language:

english

File:

PDF, 2.45 MB

english, 2016

21

SPIE Proceedings [SPIE SPIE Optical Engineering + Applications - San Diego, California, United States (Sunday 25 August 2013)] Polarization Science and Remote Sensing VI - Extracting the inclination angle of nerve fibers within the human brain with 3D-PLI independent of system properties

Reckfort, Julia, Wiese, Hendrik, Dohmen, Melanie, Grässel, David, Pietrzyk, Uwe, Zilles, Karl, Amunts, Katrin, Axer, Markus, Shaw, Joseph A., LeMaster, Daniel A.

Year:

2013

Language:

english

File:

PDF, 2.13 MB

english, 2013

22

[IEEE 2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017) - Melbourne, Australia (2017.4.18-2017.4.21)] 2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017) - Registration of ultra-high resolution 3D PLI data of human brain sections to their corresponding high-resolution counterpart

Ali, Sharib, Rohr, Karl, Axer, Markus, Amunts, Katrin, Eils, Roland, Worz, Stefan

Year:

2017

Language:

english

File:

PDF, 1.57 MB

english, 2017

23

SPIE Proceedings [SPIE European Conferences on Biomedical Optics - Munich, Germany (Sunday 25 June 2017)] Novel Biophotonics Techniques and Applications IV - Correlative polarized light imaging and two-photon fluorescence microscopy for 3D myelinated fibers reconstruction

Amelink, Arjen, Vitkin, I. Alex, Costantini, Irene, Menzel, Miriam, Silvestri, Ludovico, Schubert, Nicole, Axer, Markus, Amunts, Katrin, Pavone, Francesco S.

Year:

2017

Language:

english

File:

PDF, 501 KB

english, 2017

24

Decoding the microstructural correlate of diffusion MRI

Caspers, Svenja, Axer, Markus

Journal:

NMR in Biomedicine

Year:

2017

Language:

english

File:

PDF, 402 KB

english, 2017

25

Post-mortem inference of the human hippocampal connectivity and microstructure using ultra-high field diffusion MRI at 11.7 T

Beaujoin, Justine, Palomero-Gallagher, Nicola, Boumezbeur, Fawzi, Axer, Markus, Bernard, Jeremy, Poupon, Fabrice, Schmitz, Daniel, Mangin, Jean-François, Poupon, Cyril

Journal:

Brain Structure and Function (Anatomy and Embryology 1891-2006)

Year:

2018

Language:

english

File:

PDF, 6.49 MB

english, 2018

26

[IEEE 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018) - Washington, DC, USA (2018.4.4-2018.4.7)] 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018) - Evaluating local features in high-resolution 3D-PLI data

Ali, Sharib, Axer, Markus, Amunts, Katrin, Eils, Roland, Rohr, Karl

Year:

2018

Language:

english

File:

PDF, 894 KB

english, 2018

27

[IEEE 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018) - Washington, DC, USA (2018.4.4-2018.4.7)] 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018) - Scale-bundle spline-based non-rigid registration for handling fissures

Ali, Sharib, Amunts, Katrin, Eils, Roland, Axer, Markus, Rohr, Karl

Year:

2018

Language:

english

File:

PDF, 493 KB

english, 2018

28

A multiscale approach for the reconstruction of the fiber architecture of the human brain based on 3D-PLI

Reckfort, Julia, Wiese, Hendrik, Pietrzyk, Uwe, Zilles, Karl, Amunts, Katrin, Axer, Markus

Journal:

Frontiers in Neuroanatomy

Year:

2015

Language:

english

File:

PDF, 2.99 MB

english, 2015

29

3D Reconstructed Cyto-, Muscarinic M2 Receptor, and Fiber Architecture of the Rat Brain Registered to the Waxholm Space Atlas

Schubert, Nicole, Axer, Markus, Schober, Martin, Huynh, Anh-Minh, Huysegoms, Marcel, Palomero-Gallagher, Nicola, Bjaalie, Jan G., Leergaard, Trygve B., Kirlangic, Mehmet E., Amunts, Katrin, Zilles, Ka

Journal:

Frontiers in Neuroanatomy

Year:

2016

Language:

english

File:

PDF, 3.90 MB

english, 2016

30

Estimating Fiber Orientation Distribution Functions in 3D-Polarized Light Imaging

Axer, Markus, Strohmer, Sven, Gräßel, David, Bücker, Oliver, Dohmen, Melanie, Reckfort, Julia, Zilles, Karl, Amunts, Katrin

Journal:

Frontiers in Neuroanatomy

Year:

2016

Language:

english

File:

PDF, 8.95 MB

english, 2016

31

High-Resolution Fiber Tract Reconstruction in the Human Brain by Means of Three-Dimensional Polarized Light Imaging

Axer, Markus, Grässel, David, Kleiner, Melanie, Dammers, Jürgen, Dickscheid, Timo, Reckfort, Julia, Hütz, Tim, Eiben, Björn, Pietrzyk, Uwe, Zilles, Karl, Amunts, Katrin

Journal:

Frontiers in Neuroinformatics

Year:

2011

Language:

english

File:

PDF, 1.32 MB

english, 2011

32

Improving the Realism of White Matter Numerical Phantoms: A Step toward a Better Understanding of the Influence of Structural Disorders in Diffusion MRI

Ginsburger, Kévin, Poupon, Fabrice, Beaujoin, Justine, Estournet, Delphine, Matuschke, Felix, Mangin, Jean-François, Axer, Markus, Poupon, Cyril

Journal:

Frontiers in Physics

Year:

2018

Language:

english

File:

PDF, 8.78 MB

english, 2018

33

Diattenuation of brain tissue and its impact on 3D polarized light imaging

Menzel, Miriam, Reckfort, Julia, Weigand, Daniel, Köse, Hasan, Amunts, Katrin, Axer, Markus

Journal:

Biomedical Optics Express

Year:

2017

Language:

english

File:

PDF, 40.04 MB

english, 2017

34

[IEEE 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018) - Washington, DC (2018.4.4-2018.4.7)] 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018) - A least squares approach for the reconstruction of nerve fiber orientations from tiltable specimen experiments in 3D-PLI

Schmitz, Daniel, Amunts, Katrin, Lippert, Thomas, Axer, Markus

Year:

2018

Language:

english

File:

PDF, 226 KB

english, 2018

35

Derivation of Fiber Orientations From Oblique Views Through Human Brain Sections in 3D-Polarized Light Imaging

Schmitz, Daniel, Muenzing, Sascha E. A., Schober, Martin, Schubert, Nicole, Minnerop, Martina, Lippert, Thomas, Amunts, Katrin, Axer, Markus

Journal:

Frontiers in Neuroanatomy

Year:

2018

Language:

english

File:

PDF, 4.72 MB

english, 2018

36

Diattenuation Imaging reveals different brain tissue properties

Menzel, Miriam, Axer, Markus, Amunts, Katrin, De Raedt, Hans, Michielsen, Kristel

Journal:

Scientific Reports

Year:

2019

Language:

english

File:

PDF, 3.39 MB

english, 2019

37

MEDUSA: A GPU-based tool to create realistic phantoms of the brain microstructure using tiny spheres

Ginsburger, Kévin, Matuschke, Felix, Poupon, Fabrice, Mangin, Jean-François, Axer, Markus, Poupon, Cyril

Journal:

Year:

2019

Language:

english

File:

PDF, 45.42 MB

english, 2019

38

Teaching NeuroImages: In vivo visualization of Edinger comb and Wilson pencils

Horn, Andreas, Ewert, Siobhán, Alho, Eduardo J.L., Axer, Markus, Heinsen, Helmut, Fonoff, Erich T., Polimeni, Jonathan R., Herrington, Todd M.

Journal:

Year:

2019

File:

PDF, 573 KB

2019

39

Publisher Correction: Diattenuation Imaging reveals different brain tissue properties

Menzel, Miriam, Axer, Markus, Amunts, Katrin, De Raedt, Hans, Michielsen, Kristel

Journal:

Scientific Reports

Year:

2019

Language:

english

File:

PDF, 727 KB

english, 2019

40

Publisher Correction: Diattenuation Imaging reveals different brain tissue properties

Menzel, Miriam, Axer, Markus, Amunts, Katrin, De Raedt, Hans, Michielsen, Kristel

Journal:

Scientific Reports

Year:

2019

File:

PDF, 727 KB

2019

41

FAConstructor: an interactive tool for geometric modeling of nerve fiber architectures in the brain

Reuter, Jan André, Matuschke, Felix, Menzel, Miriam, Schubert, Nicole, Ginsburger, Kévin, Poupon, Cyril, Amunts, Katrin, Axer, Markus

Journal:

International Journal of Computer Assisted Radiology and Surgery

Year:

2019

Language:

english

File:

PDF, 4.78 MB

english, 2019

42

[IEEE 2019 IEEE 9th Symposium on Large Data Analysis and Visualization (LDAV) - Vancouver, BC, Canada (2019.10.21-2019.10.21)] 2019 IEEE 9th Symposium on Large Data Analysis and Visualization (LDAV) - Parallel Particle Advection and Lagrangian Analysis for 3D-PLI Fiber Orientation Maps

Demiralp, Ali C., Zielasko, Daniel, Axer, Markus, Vierjahn, Tom, Kuhlen, TorstenW.

Year:

2019

Language:

english

File:

PDF, 4.79 MB

english, 2019

43

Analytical and Fast Fiber Orientation Distribution Reconstruction in 3D-Polarized Light Imaging

Alimi, Abib, Deslauriers-Gauthier, Samuel, Matuschke, Felix, MÃ¼ller, Andreas, Muenzing, Sascha E.A., Axer, Markus, Deriche, Rachid

Journal:

Medical Image Analysis

Year:

2020

File:

PDF, 13.29 MB

2020