mass spec imaging

classifying tumors using proteomics, imaging and deep learning

cell shape dynamics

analysis of dynamically changing cell shape for phenotypic profiling

HER2 status detection

detection of HER2 amplification status from FISH images

cell tracking

segmentation and tracking of haematopoetic stem cells in video microscopy

virtual microscopy

from simulations to microscopy images using GANs

tissue modeling

development and support for multiscale multicell simulator Morpheus

dental age estimation

estimating age from radiographs using Bayesian deep learning



(2020). Quantification of Nematic Cell Polarity in Three-dimensional Tissues. PLoS Computational Biology.

PLoS Computational Biology

(2020). An interpretable automated detection system for FISH-basedHER2 oncogene amplification testing in histo-pathologicalroutine images of breast and gastric cancer diagnostics. MIDL 2020 (medical imaging with deep learming).


(2019). Haematopoietic stem cells in perisinusoidal niches are protected from ageing. Nature Cell Biology.

Nature Cell Biology

(2019). Liquid-crystal organization of liver tissue. eLIFE 2019;8:e44860.


(2019). Forensic age estimation with Bayesian convolutional neural networks based on panoramic dental X-ray imaging. Medical Imaging with Deep Learning (MIDL).


(2019). Quantification of Nematic Cell Polarity in Three-dimensional Tissues. arXiv.


(2019). Statistical and mathematical modeling of spatiotemporal dynamics of stem cells. In Stem Cell Mobilization (pp. 219-243). Humana, New York, NY. G. Klein, P. Wuchter (Eds.) Methods in Molecular Biology. ISSN: 1064-3745. arXiv preprint arXiv:1809.01708.

Methods in Molecular Biology Preprint


Problem Suppose you found your favorite data set on Kaggle, but it is multiple gigabytes and you need it on your deep learning machine, not your local laptop. You cannot simply use wget because you need to be logged in to Kaggle. Solution The solution is to export your cookies and tell wget to use your cookies when downloading the data. To export your cookies, install the chrome extension called cookietxt-export and do the following:



MLC Seminar on 'Deep Learning in Biomedical Imaging'
Thu, 8 Nov 2018 09:00
Modelling and Simulation Tools in Systems Biology @ ICSB 2018
Sat, 27 Oct 2018 09:00
Deep learning bootcamp @ Max Planck Institute
Mon, 24 Sep 2018 08:30