Our lab combines light & electron microscopy, transcription imaging and deep sequencing with computer vision and software development. We develop tools and solutions in order to study and model transcriptional regulation in development using C. elegans and other major model organisms.

We develop software in the context of ImgLib2, Fiji, and BigDataViewer and provide it open-source to the community.

Our lab is a part of the Berlin Institute of Medical System Biology (BIMSB), MDC, Berlin.

Lab Updates:

Next Microscopy Club meeting

November 15. Digital images and their analysis, by Christopher Schmied (Cellular Imaging Core Facility, FMP). mClub page

circRTrain Course - Tissue Clearing, Lightsheet Microscopa and Data Handling

circRTrain students join the workshop organized by Stephan and Andrew Woehler. Read more

New collaborating PhD student - Peter Hirst

Peter is a new shared PhD student together with the Kainmüller lab. Read more

New Publication: MTrack

Our new paper is out - MTrack: Automated Detection, Tracking, and Analysis of Dynamic Microtubules. Read more

New Publication: BigStitcher

Our new paper is out - BigStitcher: Reconstructing high-resolution image datasets of cleared and expanded samples. Read more

HFSP Grant

HFSP has provided 900,000$ in funding for a project on quantitative dissection of molecular determinants of enhancer function. Read more


NVIDIA contributed a Quadro P6000 graphics card to support the research of Stephan, Klim, and Ella.

Marwan Zouinkhi Has Joined Our Lab!

Marwan is a new PhD student in the lab. He’s developing software and imaging strategies to quantify circRNA expression in terabyte sized reconstructions of whole animal lightsheet microscopy acquisitions. Read more
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