Patrick Scheibe

Patrick Scheibe

Creator of the Mathematica Plugin for IntelliJ IDEA. I’m a data-analyzing scientist at day and everything else at night.

Scientific Manuscripts

  • Siawoosh Mohammadi, Tobias Streubel, Leonie Klock, Luke J. Edwards, Antoine Lutti, Kerrin J. Pine, Sandra Weber, Patrick Scheibe, Gabriel Ziegler, Jürgen Gallinat, Simone Kühn, Martina F. Callaghan, Nikolaus Weiskopf, Karsten Tabelow, Error quantification in multi-parameter mapping facilitates robust estimation and enhanced group level sensitivity, NeuroImage, Volume 262, 1053-8119, (Jul. 2022), 10.1016/j.neuroimage.2022.119529

  • Jana Schor, Patrick Scheibe, Matthias Bernt, Wibke Busch, Chih Lai, Jörg Hackermüller, AI for predicting chemical-effect associations at the universe level - deepFPlearn, Briefings in Bioinformatics, Volume 23, Issue 5, (Sep. 2022), 10.1093/bib/bbac257

  • Albert Rich, Patrick Scheibe and Nasser Abbasi, Rule-based integration: An extensive system of symbolic integration rules, Journal of Open Source Software, Volume 3, Issue 32, (Dec. 2018), 10.21105/joss.01073

  • Susanne Pauline Roth, Susanna Schubert, Patrick Scheibe, Claudia Groß, Walter Brehm, and Janina Burk. Growth Factor-Mediated Tenogenic Induction of Multipotent Mesenchymal Stromal Cells Is Altered by the Microenvironment of Tendon Matrix, Cell Transplantation, Volume 27, Issue 10, 1434–50, (Oct. 2018), 10.1177/0963689718792203

  • Luisa Brandt, Susanna Schubert, Patrick Scheibe, Walter Brehm, Jan Franzen, Claudia Gross, Janina Burk, Tenogenic Properties of Mesenchymal Progenitor Cells Are Compromised in an Inflammatory Environment, International Journal of Molecular Sciences, Volume 19, Issue 9, 2549, (Aug. 2018), 10.3390/ijms19092549

  • Marcus Wagner, Patrick Scheibe, Mike Francke, Beatrice Zimmerling, Katharina Frey, Mandy Vogel, Stephan Luckhaus, Peter Wiedemann, Wieland Kiess, Franziska G. Rauscher, Automated detection of the choroid boundary within {OCT} image data using quadratic measure filters, Journal of Biomedical Optics, Volume 22, Issue 2, (Feb. 2017), 10.1117/1.jbo.22.2.025004

  • Karsten Winter, Patrick Scheibe, R. F. Guthoff, Stephan Allgeier, Oliver Stachs, Morphometrische Charakterisierung des subbasalen Nervenplexus, Der Ophthalmologe, Volumne 114, Issue 7, 608-616, (Jul. 2017), 10.1007/s00347-017-0465-3

  • Katharina Frey, Beatrice Zimmerling, Patrick Scheibe, Franziska G Rauscher, Andreas Reichenbach, Mike Francke, Robert Brunner, Does the foveal shape influence the image formation in human eyes?, Advanced Optical Technologies, Volume 6, Issue 5, 403-410, (2017), open source, 10.1515/aot-2017-0043

  • Karsten Winter, Patrick Scheibe, Bernd Köhler, Stephan Allgeier, Rudolf F. Guthoff and Oliver Stachs, Local Variability of Parameters for Characterization of the Corneal Subbasal Nerve Plexus, Current Eye Research 2, 186-198, (2016), 10.3109/02713683.2015.1010686

  • Patrick Scheibe, Maria Teresa Zocher, Mike Francke, Franziska Georgia Rauscher, Analysis of foveal characteristics and their asymmetries in the normal population, Experimental Eye Research, Volume 148, (2016), DOI:10.1016/j.exer.2016.05.013. (download pdf).

  • Patrick Scheibe, Anfisa Lazareva, Ulf-Dietrich Braumann, Andreas Reichenbach, Peter Wiedemann, Mike Francke and Franziska Georgia Rauscher, Parametric model for the 3D reconstruction of individual fovea shape from OCT data, Experimental Eye Research, 19-26, (2014), 10.1016/j.exer.2013.11.008 (download pdf).

  • Marco Weber, Nico Scherf, Thomas Kahl, Ulf-Dietrich Braumann, Patrick Scheibe, Jens-Peer Kuska, Ronny Bayer, Andreas Büttner and Heike Franke, Quantitative analysis of astrogliosis in drug-dependent humans, Brain Research, 72-87, (2013), 10.1016/j.brainres.2012.12.048

  • Shibashish Giri, Ulf-Dietrich Braumann, Priya Giri, Ali Acikgöz, Patrick Scheibe, Karen Nieber and Augustinus Bader, Nanostructured self-assembling peptides as a defined extracellular matrix for long-term functional maintenance of primary hepatocytes in a bioartificial liver modular device, International Journal of Nanomedicine, 1525-1539, (2013)

  • Nico Scherf, Christian Ludborzs, Konstantin Thierbach, Jens-Peer Kuska, Ulf-Dietrich Braumann, Patrick Scheibe, Tilo Pompe, Ingmar Glauche and Ingo Roeder, FluidTracks - Combining Nonlinear Image Registration and Active Contours for Cell Tracking, Bildverarbeitung für die Medizin 2012: Algorithmen,Systeme, Anwendungen. Proceedings des Workshops vom 18. bis 20. März 2012 in Berlin, 57-62, (2012), 10.1007/978-3-642-28502-8_12.

  • Patrick Scheibe, Philipp Wüstling, Christian Voigt, Thomas Hierl and Ulf-Dietrich Braumann, Inkrementelle lokal-adaptive Binarisierung zur Unterdrückung von Artefakten in der Knochenfeinsegmentierung, Bildverarbeitung für die Medizin 2012: Algorithmen,Systeme, Anwendungen. Proceedings des Workshops vom 18. bis 20. März 2012 in Berlin, 189-194, (2012), 10.1007/978-3-642-28502-8_34. (download pdf).

  • Markus Loeffler, Lars Greulich, Patrick Scheibe, Philip Kahl, Zaki Shaikhibrahim, Ulf-Dietrich Braumann, Jens-Peer Kuska and Nicolas Wernert, Classifying Prostate Cancer Malignancy by Quantitative Histomorphometry, The Journal of Urology 5, 1867-1875, (2012), 10.1016/j.juro.2011.12.054

  • Patrick Scheibe, Tino Wetzig, Jens-Peer Kuska, Markus Löffler, Jan C. Simon, Uwe Paasch and Ulf-Dietrich Braumann, 3D-Reconstruction of Basal Cell Carcinoma, Biomedical Image Registration: 4th International Workshop, WBIR 2010, Lübeck, Germany, July 11-13, 2010. Proceedings, 25-36, (2010), 10.1007/978-3-642-14366-3_3. (download pdf)

  • Patrick Scheibe, Ulf-Dietrich Braumann, Jens-Peer Kuska, Markus Löffler, Jan C. Simon, Uwe Paasch and Tino Wetzig, Image-processing chain for a three-dimensional reconstruction of basal cell carcinomas, Experimental Dermatology 7, 689-691, (2010), 10.1111/j.1600-0625.2010.01100.x

  • Olaf Minet, Patrick Scheibe and Urszula J. Zabarylo, Diagnosis of rheumatoid arthritis using light: correction of motion artefacts and color visualization of multispectral images, Journal of Biophotonics 3, 130-137, (2010), 10.1002/jbio.200900092

  • Olaf Minet, Patrick Scheibe, Jürgen Beuthan and Urszula Zabarylo, Correction of motion artefacts and pseudo colour visualization of multispectral light scattering images for optical diagnosis of rheumatoid arthritis, Proc. SPIE, 75470B-75470B-8, (2009), 10.1117/12.852899.

  • Jens-Peer Kuska, Patrick Scheibe and Ulf-Dietrich Braumann, Fluid Extensions for Optical Flow and Diffusion-Based Image Registration, Bildverarbeitung für die Medizin 2008: Algorithmen, Systeme, Anwendungen Proceedings des Workshops vom 6.-8. April 2008 in Berlin, 92-96, (2008), 10.1007/978-3-540-78640-5_19. (download pdf).

  • J. P. Kuska, P. Scheibe and U. D. Braumann, Fast fluid extensions for image registration algorithms, 15th IEEE International Conference on Image Processing, 2008, 2408-2411, (2008), 10.1109/ICIP.2008.4712278. (download pdf).

  • Patrick Scheibe, Ulf-Dietrich Braumann and Jens-Peer Kuska, Projection Technique for Vortex-Free Image Registration, Bildverarbeitung für die Medizin 2007, Algorithmen, Systeme, Anwendungen, Proceedings des Workshops vom 25.-27. März 2007 in München, 439-443, (2007), 10.1007/978-3-540-71091-2_88. (download pdf).

Presentations at Mathematica events

  • When Mathematica uses the graphics card - How to use CUDA with Mathematica. This was a presentation I gave at the 2nd Mathematica-day in Leipzig on September 24th. I showed the whole process of integrating the gpu-calculations into Mathematica and used julia-sets and a rigid registration as example. The presentation notebook and the required Mathematica-package is available in CUDALecture.tar.gz (5MB).

  • The Droste-Effect - How to use the Wolfram Link Library. That talk was given at the 12. Mathematica-day in Berlin (November 2010) and it shows how the the basic, radial Droste-Effect works and how it can be implemented using the Wolfram Link Library of Mathematica 8.0. This file includes the whole talk and all preparation material including a small Mathematica package and C-sources can be found in DrosteEffect.tar.gz (7MB).

  • Ring-design with Mathematica. That talk was given at the 13. Mathematica-day in Berlin (December 2011). The presentation shows how to design unique patterns using persons names and model them onto a 3d visualization of a ring. While the approach itself is very simple, the presentation shows how to use the dynamic features of Mathematica beyond the trivial cases. The Wolfram computable document: RingDesign.cdf (2.5MB).

  • Tweaking the Autocompletion of Mathematica. This talk was at the 13. Mathematica-day in Berlin. I showed that it was possible to improve the automcompletion feature of Mathematica by injecting code into the communication between front end and kernel. Unfortunately, this trick was only possible to a very specific behavior of the Mathematica version 9.0.0 and earlier. For an extended discussion please read the post on Mathematica.stackexchange and visit my GitHub repository.

PhD Thesis

A Parametric Model for the Analysis and Quantification of Foveal Shapes

ps_thesis.pdf (13 MB)

Abstract

Recently, the advance of OCT enables a detailed examination of the human retina in-vivo for clinical routine and experimental eye research. One of the structures inside the retina of immense scientific interest is the fovea, a small retinal pit located in the central region with extraordinary visual resolution. Today, only a few investigations captured foveal morphology based on a large subject group by a detailed analysis employing mathematical models.

In this work, we develop a parametric model function to describe the shape of the human fovea. Starting with a detailed discussion on the history and present of fovea research, we define the requirements for a suitable model and derive a function which can represent a broad range of foveal shapes. The model is one-dimensional in its basic form and can only account for the shape of one particular section through a fovea. Therefore, we apply a radial fitting scheme in different directions which can capture a fovea in its full three-dimensional appearance. Highly relevant foveal characteristics, derived from the model, provide valuable descriptions to quantify the fovea and allow for a detailed analysis of different foveal shapes.

To put the theoretical model into practice, we develop a numerical scheme to compute model parameters from retinal OCT scans and to reconstruct the shape of an entire fovea. For the sake of scientific reproducibility, this section includes implementation details, examples and a discussion of performance considerations.

Finally, we present several studies which employed the fovea model successfully. A first feasibility study verifies that the parametric model is suitable for foveal shapes occurring in a large set of healthy human eyes. In a follow-up investigation, we analyse foveal characteristics occurring in healthy humans in detail. This analysis will concern with different aspects including, e.g. an investigation of the fovea’s asymmetry, a gender comparison, a left versus right eye correlation and the computation of subjects with extreme foveal shapes. Furthermore, we will show how the model was used to support investigations unrelated to the direct quantification of the fovea itself. In these investigations we employed the model to compute anatomically correct regions of interest in an analysis of the OCT and the calculation of an average fovea for an optical simulation of light rays. We will conclude with currently unpublished data that shows the fovea modelling of hunting birds which have unusual, funnel-like foveal shapes.

Diploma Thesis

Projection Technique for Vortex-Free Image Registration.

diploma_final.pdf (12 MB)

Abstract

One important application of image processing in medicine is to register tissue samples onto another. Registering these high textured images with non-parametric methods leads sometimes to solutions which are known to be suboptimal.

This thesis is concerned with a novel approach for image registration. We present a projection technique for a curvature based non-parametric registration method which suppresses unwanted vortices in the displacement field. This new strategy does not change the registration method itself but it continuously leads the process of registration to a vortex-free solution.

The grounding method was introduced in [Ami94], used in [BK05] and extended in [BK06] with a vortex suppression term. Our new method calculates a Helmoltz decomposition on the intermediate steps and projects out unwanted vortices. This thesis describes the whole process of the image registration. Starting from the mathematical description of the Helmholtz decomposition, its variational presentation and the consequential partial differential equation, we will go on by looking at the discrete approximation, parts of the implementation and the application on images. Finally the results in comparison with the two other methods of Kuska and Braumann [BK05, BK06] are presented. For this purpose, samples are given and deformed with an artificial transformation. We will use these results and discover general properties, advantages and drawbacks of the different approaches.