Ignacio Arganda‐Carreras

PhenoMe provides an open-source framework for analyzing microscopy images using foundation model-derived embeddings and experimental metadata to enable phenotyping and data exploration.

DINOSim detects and segments objects in microscopy images without annotated data, achieving performance comparable to supervised methods using a pretrained DINOv2 encoder and k-nearest neighbors refinement.

The paper presents a challenge for 3D registration of expansion microscopy volumes, evaluates top methods, and highlights future directions for ExM registration.

The paper shows that during Drosophila dorsal closure, apical surface expansion in dorsal cells, regulated by Rab11 and the Dpp/Brinker pathway, confines tissue deformation under stretch.

MitoEM 2.0 provides a benchmark for 3D mitochondria segmentation in EM images with diverse datasets and standardized labels for model evaluation and comparison.

This study maps over 85,000 oocytes in mouse ovaries across their reproductive lifespan, revealing spatial patterns and a bimodal size distribution, along with a mathematical model of oocyte activation and loss.

The paper shows that wound healing in Drosophila involves reversible chromatin-lamina dewetting triggered by mechanical changes, leading to cellular contraction and tissue repair.

BiaPy provides an open-source library for deep learning in bioimage analysis, offering tools for 2D/3D image data with multi-GPU support and customizable workflows.

This study examines how neuroanatomy and synaptic clusters influence behavioural plasticity in Argentine ants under varying environmental complexity.

The paper develops self-supervised Vision Transformers for predicting fluorescence images from label-free transmitted light microscopy inputs, using the LightMyCells challenge as a benchmark.

CartoCell is a deep learning pipeline that analyzes 3D epithelial images to quantify cell morphology and packing patterns, revealing insights into tissue self-organization.

The paper investigates how energy drivers affect 3D cellular connectivity in tubular epithelia and identifies a biophysical principle linking tissue geometry and energetics to average cellular connectivity.

This paper introduces a method using X-ray phase-contrast tomography to analyze 3D morphology of amyloid-β plaques in Alzheimer's disease mouse models and identifies differences in plaque characteristics across strains.

The paper introduces SynTagMA, a tool to mark active synapses in a 2-second window, and provides software for analyzing large datasets of synaptic activity.