Löıc A. Royer

gene2fish: a multi-gene spatial expression browser for in situ hybridization data across zebrafish development

gene2fish arranges 53,595 Thisse in situ hybridization images of 8,263 zebrafish genes into a gene-by-stage grid, with anatomy-term search for validating scRNA-seq markers.

Luxar: Gaussian splatting for microscopy and scalable interactive web visualisation of multidimensional scientific data

Luxar compresses volumetric microscopy data into compact archives for interactive web visualization without requiring specialized software.

A multimodal perturbation atlas defines the phenotypic resolution of cellular morphology.

The paper presents a multimodal perturbation atlas using CRISPR knockouts in A549 cells, combining microscopy, phase imaging, and scRNA-seq to assess phenotypic resolution.

Single-cell transcriptional dynamics in a living vertebrate

This study measures single-cell transcriptional dynamics in zebrafish embryos using MS2-MCP labeling and light sheet microscopy, revealing discrete transcriptional bursts in the segmentation clock.

Tabular Foundation Models Are Competitive Cellular Perturbation Predictors Across Biological Scales

This paper evaluates Tabular Foundation Models against specialized models for predicting cellular perturbation responses across multiple biological scales and tasks.

Challenges and Progress in RNA Velocity: Comparative Analysis Across Multiple Biological Contexts

This study compares five RNA velocity methods across three datasets to evaluate their performance in predicting cellular states.

DanioDecima: A DNA sequence-to-function model of zebrafish embryogenesis

DanioDecima improves gene expression prediction in zebrafish by transferring knowledge from human and mouse models, enhancing correlations and generating synthetic promoters with expected lineage-specific motifs.

PCM1 conveys centrosome asymmetry to polarized endosome dynamics in regulating daughter cell fate

This study shows that Pcm1 regulates asymmetric endosome dynamics and RGP fate by coordinating Rab5b and Rab11a endosome markers and Par-3/dynein complexes in zebrafish and human brain organoids.

inTRACKtive - A Web-Based Tool for Interactive Cell Tracking Visualization

inTRACKtive provides a web-based tool for interactive visualization and sharing of large 3D cell tracking datasets without requiring software installation or data downloads.

Ultrack: pushing the limits of cell tracking across biological scales

Ultrack improves cell tracking across 2D, 3D, and multi-channel time-lapse recordings by integrating multiple segmentations and temporal consistency, achieving state-of-the-art performance on benchmark datasets.

Zebrahub-Multiome: Uncovering Gene Regulatory Network Dynamics During Zebrafish Embryogenesis

The paper presents Zebrahub-Multiome, a single-cell multiomic atlas of zebrafish embryogenesis, revealing gene regulatory network dynamics and cis-regulatory elements across developmental stages.

Repeated extrinsic and anisotropic mechanical inputs promote polarized adherens junction elongation

This study shows how muscle contractions and anisotropic tension drive polarized elongation of epidermal adherens junctions in C. elegans embryos.

OME-Zarr: a cloud-optimized bioimaging file format with international community support

This paper describes OME-Zarr, a cloud-optimized bioimaging file format developed through community collaboration to improve scalability and data access.

Zebrahub - Multimodal Zebrafish Developmental Atlas Reveals the State Transition Dynamics of Late Vertebrate Pluripotent Axial Progenitors

Zebrafish embryos sequenced individually across ten developmental stages, paired with light-sheet lineage reconstruction, form an atlas and browser for in silico fate mapping.

High-Resolution, Large Imaging Volume, and Multi-View Single Objective Light-Sheet Microscopy

This paper introduces a novel single objective light-sheet microscope that achieves high resolution, large field of view, and multi-view imaging for various biological systems.

ZAF -- The First Open Source Fully Automated Feeder for Aquatic Facilities

The paper introduces ZAF, an open-source automated feeding system for aquatic facilities, which provides standardized food distribution and is adaptable to various laboratory environments.

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.

Fusion of Drosophila oocytes with specified germline sister cells

The paper describes the fusion of specific Drosophila nurse cells with the oocyte and its implications for oocyte development.

Optical Aberration Correction via Phase Diversity and Deep Learning

This paper introduces a deep learning framework for correcting optical aberrations in microscopy by estimating wavefront phases and performing blind deconvolution.

CLIJ: GPU-accelerated image processing for everyone

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

Molecular Cross-Validation for Single-Cell RNA-seq

The paper introduces molecular cross-validation to select and calibrate denoising methods for single-cell RNA-seq data without ground-truth, showing it correctly identifies optimal parameters and best methods.

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.