Long Chen, Martin Strauch, Matthias Daub, Hans-Georg Luigs, Marcus Jansen and Dorit Merhof$
Learning to Segment Fine Structures Under Image-Level Supervision With an Application to Nematode Segmentation
In: International Engineering in Medicine and Biology Conference (EMBC)

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 and Carolyn S. McBride
Mosquito brains encode unique features of human odour to drive host seeking
In: Nature

Dimitrios Kapsokalyvas, Rodrigo Rosas, Rob Janssen, Jo Vanoevelen, Miranda Nabben, Martin Strauch, Dorit Merhof and Marc van Zandvoort
Multiview deconvolution approximation multiphoton microscopy of tissues and zebrafish larvae.
In: Scientific Reports 11 (10160)

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
In: eLife 10:e62885

Long Chen, Matthias Daub, Hans-Georg Luigs, Marcus Jansen, Martin Strauch and Dorit Merhof
High-throughput Phenotyping of Nematode Cysts
In: Frontiers in Plant Science

Michael Gadermayr, Lotte Heckmann, Kexin Li, Friederike Bähr, Madlaine Müller, Daniel Truhn, Dorit Merhof and Burkhard Gess
Image-to-Image Translation for Simplified MRI Muscle Segmentation
In: Frontiers in Radiology

Michael Gadermayr, Maximilian Tschuchnig, Laxmi Gupta, Nils Krämer, Daniel Truhn, Dorit Merhof and Burkhard Gess
An asymmetric cycle-consistency loss for dealing with many-to-one mappings in image translation: a study on thigh MR scans
In: IEEE International Symposium on Biomedical Imaging (ISBI)

Michael Schleyer, Alice Weiglein, Juliane Thoener, Martin Strauch, Volker Hartenstein, Melisa Kantar Weigelt, Sarah Schuller, Timo Saumweber, Katharina Eichler, Astrid Rohwedder, Dorit Merhof, Marta Zlatic, Andreas Stefan Thum and Bertram Gerber
Identification of dopaminergic neurons that can both establish associative memory and acutely terminate its behavioral expression
In: Journal of Neuroscience 40 (31)

Daniel Bug, Gregor Nickel, Anne Grote, Friedrich Feuerhake, Eva Oswald, Julia Schüler and Dorit Merhof
Image Quilting for Histological Image Synthesis
In: Bildverarbeitung für die Medizin (BVM)

Daniel Bug, Felix Bartsch, Nadine Sarah Schaadt, Mathias Wien, Friedrich Feuerhake, Julia Schüler, Eva Oswald and Dorit Merhof
Scalable HEVC for Histological Whole-Slide Image Compression
In: Bildverarbeitung für die Medizin (BVM)

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
In: IEEE International Symposium on Biomedical Imaging (ISBI)

Long Chen, Weiwen Zhang, Yuli Wu, Martin Strauch and Dorit Merhof
Semi-supervised Instance Segmentation with a Learned Shape Prior
In: MICCAI Workshop on Medical Image Learning with Less Labels and Imperfect Data (MIL3ID)

Barbara M. Klinkhammer Nassim Bouteldja and Dorit Merhof
Deep Learning-Based Segmentation and Quantification in Experimental Kidney Histopathology
In: Journal of the American Society of Nephrology

Michael Gadermayr, Ann-Kathrin Dombrowski, Barbara Mara Klinkhammer, Peter Boor and Dorit Merhof
CNN Cascades for Segmenting Sparse Objects in Gigapixel Whole Slide Images
In: Computerized Medical Imaging and Graphics 71

Michael Gadermayr, Laxmi Gupta, Vitus Appel, Peter Boor, Barbara Mara Klinkhammer and Dorit Merhof
Generative Adversarial Networks for Facilitating Stain-Independent Supervised & Unsupervised Segmentation: A Study on Kidney Histology
In: IEEE Transactions on Medical Imaging

V. Gerber, L. Yang, M. Takamiya, V. Ribes, V. Gourain, R. Peravali, J. Stegmaier, R. Mikut, M. Reischl, M. Ferg and U. Strähle
The HMG Box Transcription Factors Sox1a and Sox1b Specify a New Class of Glycinergic Interneuron in the Spinal Cord of Zebrafish Embryos
In: Development 146 (4)

Laxmi Gupta, Barbara Mara Klinkhammer, Peter Boor, Dorit Merhof and Michael Gadermayr
Iterative learning to make the most of unlabeled and quickly obtained labeled data in histology
In: 2nd International Conference on Medical Imaging with Deep Learning (MIDL)

Michael Gadermayr, Laxmi Gupta, Barbara Mara Klinkhammer, Peter Boor and Dorit Merhof
Unsupervisedly Training GANs for Segmenting Digital Pathology with Automatically Generated Annotations
In: 2nd International Conference on Medical Imaging with Deep Learning (MIDL)

Nassim Bouteldja, Dorit Merhof, Jan Ehrhardt and Mattias P. Heinrich
Deep Multi-Modal Encoder-Decoder Networks for Shape Constrained Segmentation and Joint Representation Learning
In: Bildverarbeitung für die Medizin (BVM)

Laura Hoppe Alvarez, Sabine Eisold, Rustam A. Gumerov, Martin Strauch, Andrey A. Rudov, Pia Lenssen, Dorit Merhof, Igor I. Potemkin, Ulrich Simon and Dominik Wöll
Deformation of Microgels at Solid-Liquid Interfaces Visualized in Three-Dimension
In: Nano Letters 19 (12)

Daniel Bug, Dennis Eschweiler, Qianyu Liu, Justus Schock, Leon Weninger, Friedrich Feuerhake, Julia Schüler, Johannes Stegmaier and Dorit Merhof
Combined Learning for Similar Tasks with Domain-Switching Networks
In: International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI)

Martin Strauch, Karl Krüger, Latha Mukunda, Alja Lüdke, C. Giovanni Galizia and Dorit Merhof
Interpolating maps between neural response spaces for chemosensing with fruit fly antenna sensors.
In: IEEE International Conference on Bioinformatics and Bioengineering (BIBE)

Long Chen, Martin Strauch, Matthias Daub, Marcus Jansen, Hans-Georg Luigs and Dorit Merhof
Instance Segmentation of Nematode Cysts in Microscopic Images of Soil Samples
In: International Engineering in Medicine and Biology Conference (EMBC)

Daniel Bug, Friedrich Feuerhake, Eva Oswald, Julia Schüler and Dorit Merhof
Semi-Automated Analysis of Digital Whole Slides from Humanized Lung-Cancer Xenograft Models for Checkpoint Inhibitor Response Prediction
In: Oncotarget

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.
In: 18th IEEE Conference on Bioinformatics and Bioengineering (BIBE)

Martin Strauch, Volker Hartenstein, Ingrid V. Andrade, Albert Cardona and Dorit Merhof
Annotated dendrograms for neurons from the larval fruit fly brain.
In: Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM)

Sascha E.A. Muenzing, Martin Strauch, James W. Truman, Katja Bühler, Andreas Thum and Dorit Merhof
larvalign: Aligning gene expression patterns from the larval brain of Drosophila melanogaster
In: Neuroinformatics 16 (1)

Michael Gadermayr, Constantin Disch, Madlaine Müller, Dorit Merhof and Burkhard Gess
A Comprehensive Study on Automated Muscle Segmentation for Assessing Fat Infiltration in Neuromuscular Diseases
In: Magnetic Reconance Imaging (MRI) 48

Michael Gadermayr, Dennis Eschweiler, Barbara Mara Klinkhammer, Peter Boor and Dorit Merhof
Gradual Domain Adaptation for Segmenting Whole Slide Images Showing Pathological Variability
In: International Conference on Image and Signal Processing (ICISP)

Michael Gadermayr, Vitus Appel, Barbara M. Klinkhammer, Peter Boor and Dorit Merhof
Which Way Round? A Study on the Performance of Stain-Translation for Segmenting Arbitrarily Dyed Histological Images
In: International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI)

Laxmi Gupta, Barbara Mara Klinkhammer, Peter Boor, Dorit Merhof and Michael Gadermayr
Stain Independent Segmentation of Whole Slide Images: A Case Study in Renal Histology
In: IEEE International Symposium on Biomedical Imaging (ISBI)

Michael Gadermayr, Dennis Eschweiler, Barbara Mara Klinkhammer, Peter Boor and Dorit Merhof
Gradual Domain Adaptation for Segmenting Whole Slide Images Showing Pathological Variability
In: International Conference on Image and Signal Processing (ICISP)

B. Mattes, Y. Dang, G. Greicius, L. T. Kaufmann, S. Özbek, B. Prunsche, J. Rosenbauer, J. Stegmaier, R. Mikut, G. U. Nienhaus, A. Schug, D. M. Virshup and S. Scholpp
Wnt/PCP Controls Spreading of Wnt/b-Catenin Signals by Cytonemes in Vertebrates
In: eLife

H. M. T. Choi, M. Schwarzkopf, M. E. Fornace, A. Acharya, G. Artavanis, J. Stegmaier, A. Cunha and N. A. Pierce
Third-Generation In Situ Hybridization Chain Reaction: Multiplexed, Quantitative, Sensitive, Versatile, Robust
In: Development

B. Schott, M. Traub, C. Schlagenhauf, M. Takamiya, T. Antritter, A. Bartschat, K. Löffler, D. Blessing, J. C. Otte, A. Y. Kobitski, G. U. Nienhaus, U. Strähle, R. Mikut and J. Stegmaier
EmbryoMiner: A New Framework for Interactive Knowledge Discovery in Large-Scale Cell Tracking Data of Developing Embryos
In: PLOS Computational Biology 14 (4)

T. Scherr, A. Bartschat, M. Reischl, J. Stegmaier and R. Mikut
Best Practices in Deep Learning-Based Segmentation of Microscopy Images
In: Proceedings 28. Workshop Computational Intelligence

T. V. Spina, J. Stegmaier, A. Falcao, E. Meyerowitz and A. Cunha
SEGMENT3D: A Web-based Application for Collaborative Segmentation of 3D Images used in the Shoot Apical Meristem
In: IEEE International Symposium on Biomedical Imaging (ISBI), Washington D.C., USA

J. Stegmaier, T. V. Spina, A. Falcao, A. Bartschat, R. Mikut, E. Meyerowitz and A. Cunha
Cell Segmentation in 3D Microscopy Images using Supervoxel Merge-Forests with CNN-based Hypothesis Selection
In: IEEE International Symposium on Biomedical Imaging (ISBI), Washington D.C., USA

Long Chen and Dorit Merhof
MixNet: Multi-modality Mix Network for Brain Segmentation
In: MICCAI Brainlesion Workshop (BrainLes)

Eugenio Martinelli, Alja Lüdke, Piergiorgio Adamo, Martin Strauch, Corrado Di Natale and C. Giovanni Galizia
Normalizing brain activity across individuals using functional reference mapping
In: Scientific Reports 7 (17128)

Dominic Siedhoff(1), Martin Strauch(1), Victoria Shpacovitch and Dorit Merhof
Unsupervised Data Analysis for Virus Detection with a Surface Plasmon Resonance Sensor
In: IEEE International Conference on Image Processing Theory, Tools and Applications (IPTA)

Jakob Unger, Mike Mansour, Marcin Kopaczka, Nina Gronloh, Marc Spehr and Dorit Merhof
An Unsupervised Learning Approach for Tracking Mice in an Enclosed Area
In: BMC Bioinformatics 18 (272)

Michael Gadermayr, Sean Steven Cooper, Barbara Klinkhammer, Peter Boor and Dorit Merhof
A Quantitative Assessment of Image Normalization for Classifying Histopathological Tissue of the Kidney
In: German Conference on Pattern Recognition (GCPR)

Michael Gadermayr, Dennis Eschweiler, Abiramjee Jeevanesan, Barbara Mara Klinkhammer, Peter Boor and Dorit Merhof
Segmenting Renal Whole Slide Images Virtually Without Training Data
In: Computers in Biology and Medicine 90

Sascha E.A. Muenzing, Andreas S. Thum, Katja Bühler and Dorit Merhof
Evaluation of multi-channel image registration of the central nervous system of Drosophila larvae
In: Bildverarbeitung für die Medizin (BVM)

Daniel Bug, Anne Grote, Julia Schüler, Friedrich Feuerhake and Dorit Merhof
Analyzing Immunohistochemically Stained Whole-Slide Images of Ovarian Carcinoma
In: Bildverarbeitung für die Medizin (BVM)

Daniel Bug, Steffen Schneider, Anne Grote, Eva Oswald, Friedrich Feuerhake, Julia Schüler and Dorit Merhof
Context-based Normalization of Histological Stains using Deep Convolutional Features
In: MICCAI International Workshop on Deep Learning in Medical Image Analysis (DLMIA)

Jakob Unger, Dorit Merhof and Susanne Renner
Computer vision applied to herbarium specimens of German trees: Testing the future utility of the two million JSTOR plant images for automated identification
In: BMC Evolutionary Biology 16 (1)

Michael Gadermayr, Barbara M. Klinkhammer, Peter Boor and Dorit Merhof
Do we Need Large Annotated Training Data for Detection Applications in Biomedical Image Data? A Case Study in Renal Glomeruli Detection
In: MICCAI Workshop on Machine Learning in Medical Imaging (MLMI)

Michael Gadermayr, Martin Strauch, Barbara Mara Klinkhammer, Sonja Djudjaj, Peter Boor and Dorit Merhof
Domain Adaptive Classification for Compensating Variability in Histopathological Whole Slide Images
In: International Conference on Image Analysis and Recognition (ICIAR)

Dennis Eschweiler, Michael Gadermayr, Jakob Unger, Markus Nippold, Björn Falkenburger and Dorit Merhof
A Feasibility Study on Automated Protein Aggregate Characterization Utilizing a Hybrid Classification Model
In: 6th Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM)

Martin Strauch, Markus Rothermel, Matt Wachowiak and Dorit Merhof
Smoothness-constrained convex cone analysis for signal extraction from calcium imaging movies
In: IEEE International Symposium on Biomedical Imaging (ISBI)

Dennis Eschweiler, Jakob Unger, Kraisorn Chaisaowong, Mugdha Sawant, Reinhard Windoffer, Rudolf E. Leube and Dorit Merhof
Detection and Quantification of Cytoskeletal Granules
In: Bildverarbeitung für die Medizin (BVM)

Daniel Bug, Julia Schüler, Friedrich Feuerhake and Dorit Merhof
Multi-class single-label classification of histopathological whole-slide images
In: IEEE International Symposium on Biomedical Imaging (ISBI)

Minmin Shen, Paul Szyszka, Oliver Deussen, C. Giovanni Galizia and Dorit Merhof
Automated Tracking and Analysis of Behavior in Restrained Insects
In: Journal of Neuroscience Methods 293

Minmin Shen, Chen Li, Wei Huang, Paul Szyszka, Kimiaki Shirahama, Marcin Grzegorzek, Dorit Merhof and Oliver Deussen
Interactive Tracking of Insect Posture
In: Pattern Recognition 48 (11)

Felix Schönenberger, Anja Deutzmann, Elisa Ferrando-May and Dorit Merhof
Discrimination of cell cycle phases in PCNA-immunolabeled cells
In: BMC Bioinformatics 16 (180)

Daniel Bug, Friedrich Feuerhake and Dorit Merhof
Foreground Extraction for Histopathological Whole-Slide Imaging
In: Bildverarbeitung für die Medizin (BVM)

Annika Zuschlag, Michail Schwab, Dorit Merhof and Giso Hahn
Transition metal precipitates in mc Si: a new detection method using 3D-FIB
In: Solid State Phenomena 205-206

Minmin Shen, Wei Huang, Paul Szyszka, C. Giovanni Galizia and Dorit Merhof
Interactive Framework for Insect Tracking with Active Learning
In: 22nd International Conference on Pattern Recognition (ICPR)

David Friedrich, Christoph Haarburger, Adrian Luna-Cobos, Dietrich Meyer-Ebrecht, Alfred Böcking and Dorit Merhof
Segmentierung von Zellkernen für Hochdurchsatz-DNA-Bildzytomerie
In: Bildverarbeitung für die Medizin (BVM)

David Friedrich, Dietrich Meyer-Ebrecht, Alfred Böcking and Dorit Merhof
Detection of felt tip markers on microscope slides
In: SPIE Medical Imaging 2014: Digital Pathology

Minmin Shen, Bastian Zimmer, Marcel Leist and Dorit Merhof
Automated Image Processing to Quantify Cell Migration
In: Bildverarbeitung für die Medizin (BVM)

Martin Strauch, Clemens Müthing, Marc P. Brög, Paul Szyska, Daniel Münch, Thomas Laudes, Oliver Deussen, C. Giovanni Galizia and Dorit Merhof
The Looks of an Odor - Visualising Neural Odor Response Patterns in Real Time
In: BMC Bioinformatics 14 (Suppl 19)

Martin Strauch, Clemens Müthing, Marc P. Brög, Paul Szyska, Daniel Münch, Thomas Laudes, Oliver Deussen, C. Giovanni Galizia and Dorit Merhof
The Looks of an Odor - Visualising Neural Odor Response Patterns in Real Time
In: BMC Bioinformatics 14 (Suppl 19)

Annika Zuschlag, Michail Schwab, Dorit Merhof and Giso Hahn
Transition metal precipitates in mc Si: a new detection method using 3D-FIB
In: Solid State Phenomena 205-206

Minmin Shen, Paul Szyszka, C. Giovanni Galizia and Dorit Merhof
Automatic framework for tracking honeybee's antennae and mouthparts from low framerate video
In: IEEE International Conference on Image Processing (ICIP)

Anne K. Krug, Nina V. Balmer, Florian Matt, Felix Schönenberger, Dorit Merhof and Marcel Leist
Evaluation of a human neurite growth assay as specific screen for developmental neurotoxicants
In: Archives of Toxicology 87 (12)

David Friedrich
Eliminating Defocused Objects From a Cell Collection Used For Early Cancer Diagnosis
In: POSTER 2013 - Proceedings of the 17th International Student Conference on Electrical Engineering

David Friedrich, Adrian Luna Cobos, Stefan Biesterfeld, Alfred Böcking and Dietrich Meyer-Ebrecht
Konturverfeinerung über Fourierdeskriptoren
In: Bildverarbeitung für die Medizin 2013

Alfred Böcking, David Friedrich, Chen Jin, André Bell, Thomas Würflinger, Dietrich Meyer-Ebrecht, Yu Zhang, Stefan Biesterfeld, Natalia Pomjanski, Leonid Berynskyy, Richard Yeung, Jörg Handschel, Branko Palcic and Til Aach
Diagnostic Cytometry
In: Oral Cytology

Marcin Moch, Gerlind Herberich, Til Aach, Rudolf E. Leube and Reinhard Windoffer
Measuring the regulation of keratin filament network dynamics
In: Proceedings of the National Academy of Sciences of the United States of America (PNAS)

Matthias Mühlich, David Friedrich and Til Aach
Supervised Quality Assessment Of Medical Image Registration: Application to intra-patient CT lung registration
In: Medical Image Analysis 16 (8)

David Friedrich, Chen Jin, Yu Zhang, Chen Demin, Li Yuan, Leonid Berynskyy, Stefan Biesterfeld, Dietrich Meyer-Ebrecht and Alfred Böcking
A Pattern Recognition System for Identifying Cancer Cells in Serous Effusions
In: Proceddings of Pathology Informatics 2012, Journal of Pathology Informatics

David Friedrich, Chen Jin, Yu Zhang, Chen Demin, Li Yuan, Leonid Berynskyy, Stefan Biesterfeld, Til Aach and Alfred Böcking
Identification of Prostate Cancer Cell Nuclei for DNA-Grading of Malignancy
In: Bildverarbeitung für die Medizin 2012

David Friedrich, Matthias Brozio, Andre Bell, Stefan Biesterfeld, Alfred Böcking and Til Aach
Nucleus fingerprinting for the unique identification of Feulgen-stained nuclei
In: SPIE Medical Imaging 2012: Computer-Aided Diagnosis

David Friedrich, Joschka zur Jacobsmühlen, Till Braunschweig, André Bell, Kraisorn Chaisaowong, Ruth Knüchel-Clarke and Til Aach
Detection of immunocytological markers in photomicroscopic images
In: SPIE Medical Imaging 2012: Computer-Aided Diagnosis

Gerlind Herberich, Reinhard Windoffer, Rudolf E. Leube and Til Aach
Signal and Noise Modeling in Confocal Laser Scanning Fluorescence Microscopy
In: International conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) - Volume Part I LNCS 7510 7510 of Lecture Notes in Computer Science

Marcin Moch Reinhard Windoffer and Rudolf E. Leube
Quantification of growth factor-dependent keratin network motility at subcellular resolution
In: Proceedings of the 9th Focus On Microscopy Conference

David Friedrich, André Bell, Kraisorn Chaisaowong, Till Braunschweig, Ruth Knüchel-Clarke and Til Aach
High Dynamic Range Microscopy for Color Selective Virtual De-Staining of Immunocytological Specimens
In: Bildverarbeitung für die Medizin 2011

André Bell, David Friedrich, Kraisorn Chaisaowong, Till Braunschweig, Ruth Knüchel-Clarke and Til Aach
Fast Virtual Destaining of Immunocytological Specimens
In: IEEE International Symposium on Biomedical Imaging (ISBI) 2011

Gerlind Herberich, Reinhard Windoffer, Rudolf Leube and Til Aach
3D Segmentation of Keratin Intermediate Filaments in Confocal Laser Scanning Microscopy
In: Proceedings of the 33rd International Conference of the IEEE Engineering in Medicine and Biology Society