projects

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

publications

more

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

OpenReview

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

arXiv

(2018). Automated detection of the HER2 gene amplification status in Fluorescence in situ hybridization images for the diagnostics of cancer tissues. Scientific Reports.

BioRxiv

(2018). Liquid-crystal organization of liver tissue. bioRxiv.

BioRxiv

(2018). Statistical and mathematical modeling of spatiotemporal dynamics of stem cells. Methods in Molecular Biology, Springer Protocols, Humana Press, 2018 (in press). arXiv preprint arXiv:1809.01708.

Preprint

(2018). Hematopoietic stem cells in perisinusoidal niches are protected from aging. Experimental Hematology, 64:S43.

DOI

(2018). Combining deep learning and active contours opens the way to robust, automated analysis of 3D brain cytoarchitectonics. Machine Learning in Medical Imaging (MLMI), LNCS 11046. bioRxiv 297689.

Preprint DOI

posts

updated on 1 min read

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:

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talks

MLC Seminar on 'Deep Learning in Biomedical Imaging'
Thu, 8 Nov 2018 09:00
MLC Seminar on ‘Deep Learning in Biomedical Imaging’
slides code
Modelling and Simulation Tools in Systems Biology @ ICSB 2018
Sat, 27 Oct 2018 09:00
COMBINE & de.NBI Tutorial: Modelling and Simulation Tools in Systems Biology
project
Deep learning bootcamp @ Max Planck Institute
Mon, 24 Sep 2018 08:30
Deep Learning Bootcamp 2018

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