Florian Jug

CALIPERS: Cell cycle-aware live imaging for phenotyping experiments and regeneration studies

CALIPERS enables cell cycle-aware live imaging by integrating a modified FUCCI variant, analysis software, and reporter lines for phenotyping and regeneration studies.

AI4Life Open Calls and Public Challenges: why, how, and what we have learned.

The paper discusses AI4Life's Open Calls and Public Challenges, highlighting the state of bioimage analysis, tool availability, and the need for better data and infrastructure.

FeatureForest: the power of foundation models, theusability of random forests

FeatureForest uses foundation model embeddings with random forests to enable fast, accurate segmentation of complex biological images with minimal labeling.

Hijacking and Integration of Algal Plastids andMitochondria in a Polar Planktonic Host

The paper tracks plastid and mitochondrial integration in a polar planktonic host over months, showing sustained benefits and highlighting a new strategy in plastid symbiosis.

MicroSplit: Semantic Unmixing of Fluorescent Microscopy Data

MicroSplit uses deep learning to computationally unmix fluorescent microscopy data, enabling faster imaging and reduced photon exposure by separating multiple cellular structures from a single channel.

Local DNA compaction creates TF-DNA clusters that enable transcription

This study shows that local DNA compaction forms TF-DNA clusters, which enable transcription by increasing TF binding sites and stabilizing the cluster.

Zyxin contributes to coupling between cell junctions and contractile actomyosin networks during apical constriction

The paper identifies ZYX-1/zyxin as a key protein linking actomyosin networks to cell-cell junctions during apical constriction in C. elegans gastrulation.

Prediction of designer-recombinases for DNA editing with generative deep learning

The paper introduces RecGen, a deep learning model that generates designer-recombinases for novel DNA target sites, outperforming traditional directed evolution methods.

BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis

The BioImage Model Zoo provides a community standard, infrastructure, and open repository for sharing, testing, and deploying pre-trained deep learning microscopy models across multiple bioimage analysis tools.

Labkit: Labeling and Segmentation Toolkit for Big Image Data

LO_SCPLOWABKITC_SCPLOW is a Fiji plugin for efficient segmentation of big image data, supporting manual and automated routines on single- and multi-channel images and timelapse movies.

Tissue scale properties of the extracellular matrix regulates nuclear shape, organisation and fate in the embryonic midline sutures

The paper investigates how extracellular matrix properties influence nuclear shape, organization, and cell fate in embryonic midline sutures through physical and genetic analyses.

Extracellular mechanical forces drive endocardial cell volume decrease during cardiac valve morphogenesis

The paper shows mechanical forces reduce endocardial cell volume during zebrafish cardiac valve formation through TRPP2/TRPV4 channels and hyaluronic acid.

ZeroCostDL4Mic: an open platform to use Deep-Learning in Microscopy

ZeroCostDL4Mic provides a platform to use deep learning in microscopy, enabling tasks like segmentation and denoising through Google Colab.

Regionalized tissue fluidization by an actomyosin cable is required for epithelial gap closure during insect gastrulation

The paper shows that during insect gastrulation, regionalized tissue fluidization by an actomyosin cable enables epithelial gap closure through cell intercalation and tension release.

CLIJ: GPU-accelerated image processing for everyone

CLIJ provides GPU-accelerated image processing through a Fiji plugin, enabling faster workflows on consumer hardware.

Content-Aware Image Restoration: Pushing the Limits of Fluorescence Microscopy

This paper demonstrates how deep learning-based image restoration extends fluorescence microscopy's capabilities by improving resolution, reducing photon exposure, and increasing frame rates.