OM_labs.md
June 25, 2026 · View on GitHub
Labs and people active in open microscopy
Lab / PI | Description | Resources |
|---|---|---|
| BiA-PoL | Robert Haase. Bio-image analysis technology development group. DFG Cluster of Excellence "Physics of Life", TU Dresden, Germany. | Homepage, Blog, Open source code, Teaching materials (slides), Teaching materials (videos) |
| Bio Foundaries | Consortium to provide large-scale, cutting-edge lab automation to biologists. | Homepage |
| Carpenter-Singh lab | Anne Carpenter and Shantanu Singh. Advanced methods and software tools to quantify and mine the rich information present in cellular images to yield biological discoveries. Broad Institute of MIT and Harvard in Cambridge, USA. | Homepage, Software and Code |
| Cimini lab | Beth Cimini. Bioimage analysis methods and training; co-develops CellProfiler and the Center for Open Bioimage Analysis (COBA). Broad Institute, Cambridge, USA. | Homepage, GitHub |
| Culley lab | Siân Culley. Quantitative and super-resolution microscopy with open analysis tools (NanoJ-SQUIRREL). King's College London, UK. | Homepage, GitHub |
| Danuser lab | Gaudenz Danuser. Molecular cell biology, live cell imaging, signal processing, computer vision. UT Southwestern Medical Center. USA. | Homepage, Software, GitHub |
| Dean lab | Kevin Dean. Department of Cell Biology. UT Southwestern Medical Center. | Homepage, GitHub |
| Eliceiri Lab (LOCI) | Kevin Eliceiri. UW–Madison. Core drivers of the open bioimaging ecosystem. LOCI leads and maintains key infrastructure including ImageJ2, Fiji, SCIFIO, and SciJava, and founded Bio-Formats. Hosts community platforms (imagej.net, image.sc, fiji.sc) and supports Micro-Manager development. Develops modern tools such as FLIMJ, PyImageJ, Appose, and OpenScan-LSM, alongside CurveAlign/CT-FIRE. Active in open standards, interoperability, and community hackathons across the global imaging community. | Homepage, GitHub (UW-LOCI), ImageJ ecosystem, Image.sc, FLIMJ, PyImageJ, Appose, OpenScan-LSM |
| Enderlein lab | Jörg Enderlein. Single-molecule spectroscopy and super-resolution microscopy. Georg-August-Universität Göttingen, Germany. | Homepage, Software, Teaching |
| Endesfelder lab | Ulrike Endesfelder. Insights into the inner life of living cells: Exploring cellular biophysics by single-molecule methods. Bonn University, Germany. | Homepage |
| Ganzinger lab | Kristina Ganzinger. Physics of Cellular Interactions. AMOLF, Amsterdam, NL. | Homepage, Microscopy, GitHub |
| Grecco lab | Hernan E. Grecco. Open software for microscope control; Optical methods to quantify and manipulate samples. University of Buenos Aires, AR. | Homepage |
| Grussmayer lab | Kristin Grußmayer. Quantitative and super-resolution fluorescence microscopy (SOFI, multiplexed and light-sheet imaging). TU Delft, the Netherlands. | Homepage, GitHub |
| Haselhoff lab | Jim Haselhoff. Synthetic Biology for engineering plant growth. University of Cambridge, UK. | Homepage, Microscopy, GitHub |
| Hohlbein lab | Johannes Hohlbein. Single-molecule stuff. BTU Cottbus-Senftenberg, Germany & Wageningen University & Research, the Netherlands. | Homepage, GitHub |
| Heilemann lab | Mike Heilemann. Structural organization of biomolecules in cells applying novel microscopic techniques that provide single-molecule sensitivity and a spatial resolution below the diffraction limit. Goethe University Frankfurt, Germany. | Homepage, Software |
| Heintzmann lab | Rainer Heintzmann. Development of techniques to measure multidimensional information in small biological objects such as cells, cellular organelles, molecules or other structures. Friedrich-Schiller-Universität Jena, Germany. | Homepage, Software |
| Henriques lab | Ricardo Henriques. Optical cell biology. Instituto Gulbenkian de Ciência, Portugal. | Homepage, GitHub |
| Holden lab | Séamus Holden. Advanced microscopy and image analysis to understand living organisms. Newcastle University, UK. | Homepage, GitHub |
| Jacquemet lab | Guillaume Jacquemet. Cell migration and cancer cell invasion studied with live microscopy and open analysis tools. Åbo Akademi University, Turku, Finland. | Homepage, GitHub |
| Jug lab | Florian Jug. Machine learning for bioimage analysis — self-supervised denoising and segmentation. Human Technopole, Milan, Italy. | Homepage, GitHub |
| Kreshuk lab | Anna Kreshuk. Machine learning for bioimage analysis; leads development of ilastik. EMBL Heidelberg, Germany. | Homepage, GitHub |
| Manley lab | Suliana Manley. Laboratory of Experimental Biophysics. EPFL, CH. | Homepage, Software |
| NeuroCyto Lab | Christophe Leterrier. NeuroCyto: the neuronal cytoskeleton in physiology and disease. INP, CNRS-Aix Marseille University, France. | Homepage, GitHub |
| Prakash lab | Manu Prakash. Curiosity-driven science. Stanford, USA. | Homepage, GitHub |
| Preibisch lab | Stephan Preibisch. Image registration, stitching and reconstruction for light-sheet and large-scale microscopy (BigStitcher, Multiview, Mastodon). HHMI Janelia, USA. | GitHub |
| QI2 lab | Douglas Shepherd. Quantitative Imaging and Inference Laboratory. Arizona State University in Tempe, USA. | Homepage, GitHub |
| Radenovic lab | Aleksandra Radenovic. Laboratory of Nanoscale Biology (LBEN): single-molecule biophysics, nanopore sensing, and super-resolution imaging with 2D materials. EPFL, Lausanne, Switzerland. | Homepage |
| Ries lab | Jonas Ries. Super-resolution microscopy for structural cell biology. Development of techniques to visualize the structure and dynamics of molecular machines in cells on the nanoscale. Main biological target: clathrin-mediated endocytosis. EMBL Heidelberg, Germany. | Homepage, Software, Resources, GitHub |
| Royer lab | Loic A. Royer. Advanced microscopy, bioimage informatics. CZ Biohub San Francisco, USA. | Homepage, GitHub |
| Saalfeld lab | Stephan Saalfeld. Scalable image processing and reconstruction for connectomics and large light-microscopy data (N5/Zarr, BigDataViewer). Janelia Research Campus, USA. | Homepage, GitHub |
| Sieben lab | Christian Sieben. Helmholtz Centre for Infection Research, Braunschweig, Germany. | Homepage, GitHub |
| Stringer & Pachitariu labs | Carsen Stringer & Marius Pachitariu. Machine-learning tools for large-scale cellular and neural imaging (Cellpose, suite2p, facemap). Janelia Research Campus, USA. | Homepage, GitHub |
| Testa lab | Ilaria Testa. Advanced optical bioimaging at Scilifelab and KTH, Solna, Sweden. | Homepage, Tools |
| Tutkus lab | Marijonas Tutkus. Advanced fluorescence microscopy imaging and hardware/software development at Vilnius University, Lithuania. | Homepage, Tools |
| Vicidomini lab | Giuseppe Vicidomini. (STED) microscopy, spectroscopy, SPAD Arrays, image analysis. Center for Human Technology, Istituto Italiano di Tecnologia. | Homepage, GitHub |
| Wählby lab | Carolina Wählby. Quantitative microscopy group. Uppsala University, Uppsala, Sweden. | Homepage, GitHub |
| Waller lab | Laura Waller. Computational imaging lab. UC Berkeley, USA. | Homepage, Optics-Fun, Open Source, GitHub |
| Weigert lab | Martin Weigert. Computational imaging and deep learning for microscopy (StarDist, CARE, Spotiflow). TU Dresden, Germany. | Homepage, GitHub |
| Wenzel lab | Tobias Wenzel. Method development team: microfluidics and bioimgaing with Open Hardware automation for cellular interactions resesarch. UC Chile, Chile. | Homepage, GitHub |
| York lab | Andrew G. York. Calico. Microscopy techniques. USA. | Homepage, GitHub |
| Zhao lab | Weisong Zhao. Building advanced optical microscopy for biomedical applications, as well as developing smart algorithms across modalities including optical microscopy, acoustic/photoacoustic imaging, and cryo-EM/ET. Harbin Institute of Technology (HIT). USA. | Homepage, GitHub |