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  • PhD Student
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  • Post-doc
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  • Undergraduate Student
  • Veterinary
  • Visiting Scientist
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  • Deputy Director of National Reference Center
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  • Director of Center
  • Director of Department
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About

I’m a trained biophysicist and develop integrated approaches combining fluorescence imaging, wetlab experiments, computerised image analysis, and mathematical modeling. We apply this methods to study RNA regulation across several scales, ranging from sub-cellular RNA localization to cell-type mapping in tissue.

I’m currently heading the Quantitative RNA imaging group.

Software

Software
Ongoing
2 Members

Comseg – Cell segmentation for spatial transcriptomics data

Florian Muller (PI)

Recent progress in image-based spatial RNA profiling enables to spatially resolve tens to hundreds of distinct RNA species with high spatial resolution. It hence presents new avenues for comprehending tissue organization. In this context, […]
Software
Completed
2 Members

FISH-quant v2: a scalable and modular tool for smFISH image analysis

Florian Muller (PI)

Regulation of RNA abundance and localization is a key step in gene expression control. Single-molecule RNA fluorescence in situ hybridization (smFISH) is a widely used single-cell-single-molecule imaging technique enabling quantitative studies of gene expression […]
Software
Completed
2 Members

FISH-quant: automatically counting transcripts in RNA-FISH images

Christophe Zimmer (PI)

A free Matlab-based toolbox to detect and count individual mRNA transcripts in single cells by automatic analysis of 3D RNA-FISH images. Software is available freely together with extensive instructions at : https://code.google.com/p/fish-quant/. The software […]

CV

EDUCATION

HDR

  • Thesis: Exploring spatio-temporal transcriptional regulation

Ph.D.

  • Graz University of Technology, Austria and National Institutes of Health (NIH), Bethesda; 2005 – 2008
  • Thesis: Quantitative analysis of the dynamic properties of chromatin associated proteins by FRAP experiments
  • Advisors: Dr. James G. McNally, Dr. Zlatko Trajanoski

M.S.

  • Computational Physics, Universität Graz, Austria, 1999 – 2005
  • Thesis: Numerical Simulations of FRAP Experiments
  • Advisors: Dr. Max Lippitsch, Dr. Zlatko Trajanoski

Publications

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