Center for Computational and Theoretical Biology

Computational Image Analysis

Welcome to the CIA (Computational Image Analysis) group at the CCTB.

Research Summary

Modern imaging methods enable us to capture biological processes in unprecedented detail and with high temporal and spatial resolution. Often, however, we face the problem to extract and quantify relevant information from the vast amount of image data generated before hypotheses can be tested and new theories and models can be developed. To this end, cutting-edge methods from pattern recognition, machine learning and high performance computing are required to efficiently handle and automatically analyse very large image data sets.

We are a new group working on computational tools to analyze, quantify, and understand biological image data (“Bioimage Bioinformatics”). We are interested in images on all scales, from high-resolution microscopy, to 3D time-lapse imaging of tissues, to movies of swarming animals. We use techniques such as automated segmentation, feature tracking and pattern recognition to reproducibly quantify large multidimensional image datasets.

In our research, we use image analysis for example...

  • to clarify the role of forces in multicellular organization and tissue development
  • to quantify and compare network-like structures in biological systems
  • to measure spatiotemporal dynamics in order to understand signaling and control mechanisms


[ 2019 ]

2019 [ nach oben ]

  • Targeted volumetric single-molecule localization microscopy of defined presynaptic structures in brain sections. Pauli, Martin; Paul, Mila M.; Proppert, Sven; Sharifi, Marzieh; Repp, Felix; Kollmannsberger, Philip; Sauer, Markus; Heckmann, Manfred; Sirén, Anna-Leena in bioRxiv (2019).
  • Automated interpretation of Cryo-EM density maps with convolutional neural networks. Mostosi, Philipp; Schindelin, Hermann; Kollmannsberger, Philip; Thorn, Andrea in bioRxiv (2019). 644476.
  • Active zone compaction for presynaptic strength. Mrestani, Achmed; Kollmannsberger, Philip; Pauli, Martin; Repp, Felix; Kittel, Robert J.; Eilers, Jens; Doose, Sören; Sauer, Markus; Sirén, Anna-Leena; Heckmann, Manfred; Paul, Mila M. in bioRxiv (2019).


[ 2019 ] [ 2018 ] [ 2017 ]

2019 [ nach oben ]

  • Towards a Connectomic Description of the Osteocyte Lacunocanalicular Network in Bone. Weinkamer, Richard; Kollmannsberger, Philip; Fratzl, Peter in Current Osteoporosis Reports (2019).
  • Surface tension determines tissue shape and growth kinetics. Ehrig, Sebastian; Bidan, Cécile M.; West, Alan; Jacobi, Cornelius; Lam, Karen; Kollmannsberger, Philip; Petersen, Ansgar; Tomancak, Pavel; Kommareddy, Krishna; Fischer, Franz Dieter; Fratzl, Peter; Dunlop, John W. C. in Science Advances (2019). 5(9) eaav9394.
  • Electron tomography of mouse LINC complexes at meiotic telomere attachment sites with and without microtubules. Spindler, Marie-Christin; Redolfi, Josef; Helmprobst, Frederik; Kollmannsberger, Philip; Stigloher, Christian; Benavente, Ricardo in Communications Biology (2019). 2(1) 376--.

2018 [ nach oben ]

  • Tensile forces drive a reversible fibroblast-to-myofibroblast transition during tissue growth in engineered clefts. Kollmannsberger, Philip; Bidan, Cécile M; Dunlop, John; Fratzl, Peter; Vogel, Viola in Science Advances (2018). 4(1) eaao4881.
  • Automated classification of synaptic vesicles in electron tomograms of C. elegans using machine learning. Kaltdorf, Kristin V; Theiss, Maria; Markert, Sebastian M; Zhen, Mei; Dandekar, Thomas; Stigloher, Christian; Kollmannsberger, Philip in PLoS one (2018). 13(10) e0205348.

2017 [ nach oben ]

  • The Small World of Osteocytes: Connectomics of the Lacuno-Canalicular Network in Bone. Kollmannsberger, Philip; Kerschnitzki, Michael; Repp, Felix; Wagermaier, Wolfgang; Weinkamer, Richard; Fratzl, Peter in New Journal of Physics (2017). 19 073019.
  • Spatial heterogeneity in the canalicular density of the osteocyte network in human osteons. Repp, Felix; Kollmannsberger, Philip; Roschger, Andreas; Kerschnitzki, Michael; Berzlanovich, Andrea; Gruber, Gerlinde M.; Roschger, Paul; Wagermaier, Wolfgang; Weinkamer, Richard in Bone Reports (2017). 6 101-108.
  • FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms. Kaltdorf, Kristin Verena; Schulze, Katja; Helmprobst, Frederik; Kollmannsberger, Philip; Dandekar, Thomas; Stigloher, Christian in PLOS Computational Biology (2017). 13(1) 1-21.
  • Coalignment of osteocyte canaliculi and collagen fibers in human osteonal bone. Repp, Felix; Kollmannsberger, Philip; Roschger, Andreas; Berzlanovich, Andrea; Gruber, Gerlinde; Roschger, Paul; Wagermaier, Wolfgang; Weinkamer, Richard in Journal of Stuctural Biology (2017). 199 177-186.