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  • Associate Professor
  • Clinical Research Assistant
  • Clinical Research Nurse
  • Clinician Researcher
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  • Dual-education Student
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  • Honorary Professor
  • Lab assistant
  • Master Student
  • MD-PhD Student
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  • Nursing Staff
  • Permanent Researcher
  • Pharmacist
  • PhD Student
  • Physician
  • Post-doc
  • Prize
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  • Research Associate
  • Research Engineer
  • Retired scientist
  • Technician
  • Undergraduate Student
  • Veterinary
  • Visiting Scientist
  • Deputy Director of Center
  • Deputy Director of Department
  • Deputy Director of National Reference Center
  • Deputy Head of Facility
  • Director of Center
  • Director of Department
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About

Our group is dedicated to developing integrated, quantitative imaging techniques that combine wetlab experiments, microscopy/instrumentation, and image analysis. We primarily focus on single RNA imaging to investigate RNA regulation across various spatial scales. Our biological questions arise from both internal projects and our network of national and international collaborations.

Projects

Project
Ongoing
4 Members

Fish&Chips

Florian Muller (PI)

Impact of microbiota on spatial gene expression along the 3D colonic barrier Spatial organization at the cellular level is a fundamental aspect of complex life, orchestrating intricate biological processes with remarkable precision. This organization […]
Project
Ongoing
5 Members

autoFISH : a modular toolbox for sequential FISH experiments

Florian Muller (PI)

We develop a complete workflow to perform automated sequential smFISH experiments on a microscope. This includes building plans for hardware, opens-source control software, and robust experimental protocols for regular and amplified FISH. Lastly, we […]

Software

Software
Completed
2 Members

RNA2seg: a generalist model for cell segmentation in image-based spatial transcriptomics

Florian Muller (PI)

Imaging-based spatial transcriptomics (IST) enables high-resolution spatial mapping of RNA species. A key challenge in IST is accurate cell segmentation to assign each RNA molecule to the right cell. Here, we present RNA2seg, a […]
Software
Completed
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 […]

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