Florian Jug

Florian Jug

Dr. Florian Jug holds a PhD in Computational Neuroscience from the Institute of Theoretical Computer Science at ETH Zurich. His research aims at pushing the boundary of what AI and machine learning can do to better analyze and quantify biological data. At HT, Dr. Jug covers the full breadth of bio-image computing, from research on novel methods for computer vision and machine learning, all the way to offering bio-image analysis as a service.

Florian Jug is a strong proponent of open access science, open AI and ML methods, and open source software. His team is a core contributor to  Fiji (~100,000 active users)  and collaboratively develops open methods such as CARENoise2VoidPN2VDivNoising, etc. He organizes scientific conferences (e.g the I2K conference), workshops (e.g. the BIC workshops at top-tier computer vision conferences) and various practical courses on machine learning for bio-image analysis (e.g. DL@MBL in Woods Hole) or microscopy (e.g. Quantitative Imaging at Cold Spring Harbor).


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  • 09/2022 - Current Biology

    Conversion of anterograde into retrograde trains is an intrinsic property of intraflagellar transport

    Cilia or eukaryotic flagella are microtubule-based organelles found across the eukaryotic tree of life. Their very high aspect ratio and crowded interior are unfavorable to diffusive transport of most components required for their assembly and maintenance. Instead, a system of intraflagellar transport (IFT) trains moves cargo rapidly up and down the cilium (Figure 1A).1, 2, 3 Anterograde IFT, from the cell body to the […]

  • 03/2021 - BioRxiv

    Intraflagellar transport trains can turn around without the ciliary tip complex

    Cilia and flagella are microtubule doublet based organelles found across the eukaryotic tree of life. Their very high aspect ratio and crowded interior are unfavourable to diffusive transport for their assembly and maintenance. Instead, a highly dynamic system of intraflagellar transport (IFT) trains moves rapidly up and down the cilium. However, the mechanism of how […]

  • 12/2020 - Journal of Cell Biology

    3D FIB-SEM reconstruction of microtubule–organelle interaction in whole primary mouse β cells

    This collaborative work is a good example for how members of our team can collaborate with biologists and technologists to improve the quantitative analysis work required to gain insights into essential processes related to human health and pathology, in this particular case into the subcellular organization of insulin producing β cells. Microtubules play a major […]

  • 11/2020 - Protein Science

    The ImageJ ecosystem: Open‐source software for image visualization, processing, and analysis

    For decades, biologists have relied on software to visualize and interpret imaging data. As techniques for acquiring images increase in complexity, resulting in larger multidimensional datasets, imaging software must adapt. ImageJ is an open‐source image analysis software platform that has aided researchers with a variety of image analysis applications, driven mainly by engaged and collaborative […]

  • 08/2020 - arXiv

    Improving Blind Spot Denoising for Microscopy

    Many microscopy applications are limited by the total amount of usable light and are consequently challenged by the resulting levels of noise in the acquired images. This problem is often addressed via (supervised) deep learning based denoising. Recently, by making assumptions about the noise statistics, self-supervised methods have emerged. Such methods are trained directly on […]