publications

peer-reviewed papers

• • Long Chen, Matthias Daub, Hans-Georg Luigs, Marcus Jansen, Martin Strauch, Dorit Merhof: “High-throughput phenotyping of nematode cysts”,
    Frontiers in Plant Science, Sec. Technical Advances in Plant Science, https://doi.org/10.3389/fpls.2022.965254, 2022
  • Long Chen, Martin Strauch, Matthias Daub, Hans-Georg Luigs, Marcus Jansen, Dorit Merhof: “Learning to Segment Fine Structures Under Image-Level Supervision With an Application to Nematode Segmentation”,
    Engineering in Medicine and Biology Conference (EMBC), Jul 11-15 2022, Glasgow, UK, IEEE, 2022
  • Zhilei Zhao, Jessica L. Zung, Annika Hinze, Alexis L. Kriete, Azwad Iqbal, Meg A. Younger, Benjamin J. Matthews, Dorit Merhof, Stephan Thiberge, Rickard Ignell, Martin Strauch, Carolyn S. McBride: “Mosquito brains encode unique features of human odour to drive host seeking”,
    Nature, 605, pp. 706-712, 2022
  • Dimitrios Kapsokalyvas, Rodrigo Rosas, Rob Janssen, Jo Vanoevelen, Miranda Nabben, Martin Strauch, Dorit Merhof, Marc van Zandvoort: “Multiview deconvolution approximation multiphoton microscopy of tissues and zebrafish larvae”,
    Scientific Reports, 11(10160), 2021
  • David Fleck, Lina Kenzler, Nadine Mundt, Martin Strauch, Naofumi Uesaka, Robert Moosmann, Felicitas Bruentgens, Annika Missel, Artur Mayerhofer, Dorit Merhof, Jennifer Spehr and Marc Spehr: “ATP activation of peritubular cells drives testicular sperm transport.”,
    eLife, 10:e62885, 2021
  • Michael Schleyer, Aliće Weiglein, Juliane Thoener, Martin Strauch, Volker Hartenstein, Melisa Kantar Weigelt, Sarah Schuller, Timo Saumweber, Katharina Eichler, Astrid Rohwedder, Dorit Merhof, Marta Zlatic, Andreas S. Thum and Bertram Gerber: “Identification of dopaminergic neurons that can both establish associative memory and acutely terminate its behavioral expression”,
    Journal of Neuroscience, 40(31), pp. 5990-6006, 2020
  • Long Chen, Weiwen Zhang, Yuli Wu, Martin Strauch, Dorit Merhof: “Semi-supervised Instance Segmentation with a Learned Shape Prior.”,
    MICCAI workshops on Interpretable and Annotation-Efficient Learning for Medical Image Computing: IMIMIC/MIL3ID/LABELS 2020, Oct 4-8 2020, Lima, Peru, LNCS vol. 12446, pp. 94-102,  Springer, 2020
  • Long Chen, Martin Strauch, Matthias Daub, Xiaochen Jiang, Marcus Jansen, Hans-Georg Luigs, Susanne Schultz-Kuhlmann, Stefan Kruessel and Dorit Merhof: “A CNN Framework Based on Line Annotations for Detecting Nematodes in Microscopic Images”,
    International Symposium on Biomedical Imaging (ISBI), Apr 3-7 2020, Iowa City, USA, IEEE, pp. 508-512, 2020
  • Martin Strauch, Karl Krüger, Latha Mukunda, Alja Lüdke, Karl Krüger, C. Giovanni Galizia, Dorit Merhof: “Interpolating maps between neural response spaces for chemosensing with fruit fly antenna sensors”,
    International Conference on Bioinformatics and Bioengineering (BIBE), Oct 28-30 2019, Athens, Greece, IEEE, 2019
  • Laura Hoppe Alvarez, Sabine Eisold, Rustam A. Gumerov, Martin Strauch, Andrey A. Rudov, Pia Lenssen, Dorit Merhof, Igor I. Potemkin, Ulrich Simon, Dominik Wöll: “Deformation of microgels at solid-liquid interfaces visualized in 3D”,
    Nano Letters, 19(12), pp. 8862–8867, 2019
  • Long Chen, Martin Strauch, Dorit Merhof: “Instance segmentation of biomedical images with an object-aware embedding learned with local constraints”,
    International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Oct 13-17 2019, Shenzen, China, LNCS vol. 11764, pp. 451-459,  Springer, 2019
  • Long Chen, Martin Strauch, Matthias Daub, Marcus Jansen, Hans-Georg Luigs, Dorit Merhof: “Instance segmentation of nematode cysts in microscopic images of soil samples”,
    Engineering in Medicine and Biology Conference (EMBC), Jul 23-27 2019, Berlin, Germany, pp. 5932-5936, IEEE, 2019
    
  • Martin Strauch, Latha Mukunda, Alja Lüdke, C. Giovanni Galizia and Dorit Merhof: “Recovering a chemotopic feature space from a group of fruit fly antenna chemosensors”,
    International Conference on Bioinformatics and Bioengineering (BIBE), Oct 29-31 2018, Taichung, Taiwan, IEEE, 2018
  • Martin Strauch, Volker Hartenstein, Ingrid Andrade, Albert Cardona, Dorit Merhof: “Annotated dendrograms for neurons from the larval fruit fly brain”,
    Workshop on Visual Computing for Biology and Medicine (VCBM), Sep 20-21 2018, Granada, Spain, EuroGraphics, 2018
  • Sascha E.A. Muenzing, Martin Strauch, James W. Truman, Katja Bühler, Andreas Thum, Dorit Merhof: “larvalign: Aligning gene expression patterns from the larval brain of Drosophila melanogaster”,
    Neuroinformatics, 16(1), pp. 65-80, 2018
  • Dominic Siedhoff¹, Martin Strauch¹, Victoria Shpacovitch, Dorit Merhof: “Unsupervised Data Analysis for Virus Detection with a Surface Plasmon Resonance Sensor”,
    International Conference on Image Processing Theory, Tools and Applications (IPTA), Nov 28 – Dec 1 2017, Montréal, Canada, pp. 1-6, IEEE, 2017 (best paper award)
  • Eugenio Martinelli, Alja Lüdke, Piergiorgio Adamo, Martin Strauch, Corrado Di Natale, C. Giovanni Galizia: “Normalizing brain activity across individuals using functional reference mapping”,
    Scientific Reports, 7 (17128), 2017
  • Michael Gadermayr, Martin Strauch, Barbara Mara Klinkhammer, Sonja Djudjaj, Peter Boor, Dorit Merhof: “Domain Adaptive Classification for Compensating Variability in Histopathological Whole Slide Images”,
    International Conference on Image Analysis and Recognition (ICIAR), Jul 13-15 2016, Póvoa de Varzim, Portugal, LNCS 9730, pp. 616-622, Springer, 2016
  • Martin Strauch, Markus Rothermel, Matt Wachowiak, Dorit Merhof: “Smoothness-constrained convex cone analysis for signal extraction from calcium imaging movies.”,
    International Symposium on Biomedical Imaging (ISBI), Apr 13-16 2016, Prague, Czech Republic, pp. 612-616, IEEE, 2016
  • Eduardo Hatano, Ahmed M. Saveer, Felipe Borrero-Echeverry, Martin Strauch, Ali Zakir, Marie Bengtsson, Bill Hansson, Rickard Ignell, Peter Anderson, Paul G. Becher, Peter Witzgall, Teun Dekker: “A herbivore-induced plant volatile interferes with host plant and mate location in moths through suppression of olfactory signalling pathways.”,
    BMC Biology, 13:75, 2015
  • Jan Beran, Arno Weiershäuser, C. Giovanni Galizia, Julia Rein, Brian H. Smith, Martin Strauch: “On piecewise polynomial regression under general dependence conditions with an application to calcium-imaging data.”,
    Sankhya Series B, Springer, Volume 76, Issue 1, pp 49-81, 2014
  • Martin Strauch¹, Alja Lüdke¹, Daniel Münch¹, Thomas Laudes, C. Giovanni Galizia, Eugenio Martinelli, Luca Lavra, Roberto Paolesse, Alessandra Ulivieri, Alexandro Catini, Rosamaria Capuano, Corrado Di Natale: “More than apples and oranges – Detecting cancer with a fruit fly’s antenna.”,
    Scientific Reports, 4:3576, 2014 
  • Martin Strauch, Clemens Müthing, Marc P. Broeg, Paul Szyszka, Daniel Münch, Thomas Laudes, Oliver Deussen, C. Giovanni Galizia, Dorit Merhof: “The looks of an odor – Visualising neural odor response patterns in real time.”,
    BMC Bioinformatics, 14(Suppl 19):S6, 2013
  • Julia Rein, Julie A. Mustard, Martin Strauch, Brian H. Smith, C. Giovanni Galizia: “Octopamine modulates activity of neural networks in the honey bee antennal lobe”,
    Journal of Comparative Physiology A, Vol 199:11, pp. 947-962, 2013
  • Martin Strauch, Julia Rein, Christian Lutz,  C. Giovanni Galizia: “Signal extraction from movies of honeybee brain activity by convex analysis: The ImageBee plugin for KNIME.”,
    BMC Bioinformatics, 14(Suppl 18):S4, 2013
  • Martin Strauch, Mathias Ditzen, C. Giovanni Galizia: “Keeping their distance? Odor response patterns along the concentration range.”,
    Frontiers in Systems Neuroscience, 6:71, 2012
  • Martin Strauch, Marc P. Broeg, Clemens Müthing, Paul Szyszka, Oliver Deussen, C. Giovanni Galizia, Dorit Merhof: “INCIDE the Brain of a Bee – Visualising Honeybee Brain Activity in Real Time by Semantic Segmentation.”, 
    Symposium on Biological Data Visualization (BioVis), Oct 14-15 2012, Seattle, USA, pp. 17-24, IEEE, 2012 (“honorable mention” award)
  • Martin Strauch, Julia Rein, C. Giovanni Galizia: “Signal extraction from movies of honeybee brain activity by convex analysis.”,
    Int. Conf. on Computational Advances in Bio and Medical Sciences (ICCABS), Feb 23-25 2012, Las Vegas, USA,  pp. 1-6, IEEE, 2012
  • Martin Strauch, C. Giovanni Galizia: “Fast PCA for processing calcium-imaging data from the brain of Drosophila melanogaster.”,
    CIKM Workshop on Data and Text Mining in Biomedical Informatics (DTMBIO), Oct 24th 2011, Glasgow, Scotland, pp. 3-10, ACM, 2011
  • C. Giovanni Galizia, Daniel Münch, Martin Strauch, Anja Nissler, Shouwen Ma: “Integrating heterogeneous odor response data into a common response model: A DoOR to the complete olfactome.”,
    Chemical Senses, volume 35, pp. 551-563, 2010 (cover of the september 2010 issue; commentary article)
  • Martin Strauch, C. Giovanni Galizia: “Registration to a neuroanatomical reference atlas – identifying glomeruli in optical recordings of the honeybee brain.”,
    German Conference on Bioinformatics (GCB), Sep 9-12 2008, Dresden, Germany, P-136, pp. 85-95, GI, 2008
  • Jochen Supper, Martin Strauch, Dierk Wanke, Klaus Harter, Andreas Zell: “EDISA: Extracting biclusters from multiple time-series of gene-expression profiles.”,
    BMC Bioinformatics, 8:334, 2007
  • Martin Strauch, Jochen Supper, Christian Spieth, Dierk Wanke, Joachim Kilian, Klaus Harter and Andreas Zell: “A Two-Step Clustering for 3-D Gene Expression Data Reveals the Main Features of the Arabidopsis Stress Response.”,
    Journal of Integrative Bioinformatics, 4(1):54, 2007

posters and talks

• Martin Strauch, Sascha E.A. Muenzing, James W. Truman, Katja Bühler, Andreas S. Thum, Dorit Merhof: “larvalign: software for aligning gene expression patterns to a standard CNS of the Drosophila larva.”, poster abstract, 11th FENS Forum of Neuroscience, 7-11 Jul 2018, Berlin, Germany
• Eduardo Hatano, Saveer Ahmed, Felipe Borrero-Echeverry, Martin Strauch, Ali Zakir, Marie Bengtsson, Bill Hansson, Rickard Ignell, Peter Anderson, Paul Becher, Peter Witzgall, Teun Dekker: “Something does not smell right: induced plant volatiles inhibit sensory input and behavioural output in insect herbivores.”, poster abstract, 24th Meeting of the European Chemoreception Research Organization (ECRO 2014), Dijon, France, Sep 10-13, 2014 (published in Chemical Senses , 40 (3): 211-297, 2015)
• Martin Strauch: “The Database of Odor Responses (DoOR) – Mapping the fruit fly’s odor space.”, invited talk at the International Workshop on Odor Spaces, Herrenhausen Palace, Hannover, Germany, Sep 4-7, 2013 (abstract published in: Flavour 3(Suppl 1):O21, 2014)
• Martin Strauch: “Visualising odors with insect brains.”, invited talk at the 4th Int. Meeting on Visualizing Biological Data (VIZBI 2013), The Broad Institute, Cambridge, MA, USA, Mar 19-22, 2013
• Martin Strauch, C. Giovanni Galizia: “ImageBee: A KNIME plugin for analysing calcium-imaging data from the honeybee antennal lobe.”, poster abstract, 105th Annual Meeting of the German Zoological Society (DZG), University of Konstanz, Germany, Sep 21-24, 2012
•  J. Henning Proske, Martin Strauch, Ana F. Silbering, Fritjof Helmchen, C. Giovanni Galizia: “Fast 3D 2-photon calcium imaging in the antennal lobe of Drosophila”, poster abstract, Focus on Microscopy (FOM): 24th International Conference on 3D Image Processing in Microscopy, University of Konstanz, Germany, Apr 17-20, 2011
• Martin Strauch, Julia Rein, C. Giovanni Galizia: “Pattern mining in spontaneous background activity from the honeybee antennal lobe.”, poster abstract, 5th Bernstein Conference for Computational Neuroscience, University of Frankfurt, Frankfurt am Main, Germany, Sep 30 – Oct 2, 2009, (published in: Front. Comput. Neurosci., doi: 10.3389/conf.neuro.10.2009.14.160)
• Martin Strauch, Christian Lutz, David Samuelson, C. Giovanni Galizia: “Connecting insect brain imaging to data mining tools – a neuroimage extension for the KNIME platform.”, poster abstract, 2nd INCF congress on Neuroinformatics, Pilsen, Czech Republic, Sep 6-8, 2009, (published in: Front. Neur., doi: 10.3389/conf.neuro.11.2009.08.020)
• Julia Rein, Martin Strauch, C. Giovanni Galizia: “Novel techniques for the exploration of the honeybee antennal lobe.“, poster abstract, 8th Meeting of the German Neuroscience Society, Göttingen, Germany, Mar 25-29, 2009
• Shouwen Ma, Martin Strauch, Daniel Münch, C. Giovanni Galizia: “DoOR – a Database of Odorant Responses.”, poster abstract, 8th Meeting of the German Neuroscience Society, Göttingen, Germany, Mar 25-29, 2009
• Ina Klinke, Julia Rein, Michael Schmuker, Martin Strauch, Thomas Nowotny, C. Giovanni Galizia, Randolf Menzel: “The Bernstein Partner project ‘Olfactory Coding’: A joint effort to reveal the neural basis of olfaction.”, poster abstract, 4th Bernstein Symposium for Computational Neuroscience, Munich, Germany, Oct 8-10, 2008 (Front. Comput. Neurosci., doi: 10.3389/conf.neuro.10.2008.01.073)
• Martin Strauch, Julia Rein, C. Giovanni Galizia: “Towards understanding olfactory information processing in the antennal lobes of Apis mellifera.”, poster abstract, 3rd Bernstein Symposium for Computational Neuroscience, University of Göttingen, Germany, Sep 24-27, 2007

 

theses

• Martin Strauch: “Column subset selection with applications to neuroimaging data.”,
  doctoral thesis in computer science, University of Konstanz, Germany, 2014
• Martin Strauch: “Identifying gene regulatory modules in Arabidopsis thaliana.”,
  Diplomarbeit (equ. Masters thesis) in bioinformatics, University of Tübingen, Germany, 2006

software & data

• ImageBee – a KNIME plugin for processing calcium imaging movies from insect brains
• DoOR – a data repository for odor responses in Drosophila melanogaster (web interface & R package)
• EDISA – biclustering of gene expression time series data (web service & Matlab code)