2D Multimodal Image Collection for Fluorescence Prediction from Transmitted Light Microscopy
Year: 2026
Type: data-paper
Abstract: We present the Light My Cells Database, a large-scale open-access collection comprising 2,574 acquisition sets and 56,984 microscopy 2D images designed to support the development of machine learning models for fluorescence prediction from transmitted light images. The dataset aggregates data from 30 independent studies conducted across 8 national imaging centers and captures a wide diversity of biological samples, imaging modalities, and acquisition systems. Each transmitted light image - recorded in bright-field, phase contrast, or differential interference contrast -is paired with at least one fluorescence image labeling key subcellular structures: nucleus, mitochondria, tubulin, or actin. All images are standardized in OME-TIFF format and annotated with rich metadata following REMBI guidelines. A dedicated preprocessing pipeline ensures dimensional harmonization, best-focus plane selection, and consistent file naming. The database reflects the variability encountered in real-life microscopy experiments, making it suited for training and benchmarking generalizable deep learning models. It is accessible via the BioImage Archive and supports a range of downstream applications, including in silico labeling, segmentation, and cell profiling from label-free imaging.
Source: Scientific Data
Authors: Dorian Kauffmann, Guillaume Gay, Julio Mateos-Langerak, Oriane Pourcelot, Virginie Georget, Maëlle Carraz, Juliette Van Dijk, Stéphanie Bosch, Elsa Castellani, Qiyan Mao, Laura Ruiz, Valentin Asei-Ceschino, Tudor Manoliu, Louis Ruel, Julia Bonnet-Gelebart, Youssef Elhabouz, Marc Tramier, Jacques Pécréaux, Jean-Bernard Fiche, David Lleres, Christine Doucet, Erwan Gandon, Yves Lutz, Bertrand Vernay, Daniel Stockholm, Abbass Jaber, Aude Moret, Romain Morichon, Mónica Fernández-Monreal, Edouard Bertrand, Emmanuel Faure
Institutions: Centre National de la Recherche Scientifique, Université de Montpellier, Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier, France-BioImaging, Inserm, Institut de Génétique Humaine, BioCampus Montpellier, Centre de Recherche en Biologie cellulaire de Montpellier, Pharmacochimie et Biologie pour le Développement, Institut de Recherche pour le Développement, Université de Toulouse, Unité de biologie Moléculaire, Cellulaire et du Développement, Centre de Biologie Intégrative de Toulouse, Institut de Biologie du Développement Marseille, Institut Gustave Roussy, Institut de génétique et de développement de Rennes, Université de Rennes, Centre de Biologie Structurale, Institut de génétique et de biologie moléculaire et cellulaire, Université de Strasbourg, École Pratique des Hautes Études, Université Paris Sciences et Lettres, Genethon (France), Université Paris-Saclay, Université d'Évry Val-d'Essonne, Centre de Recherche Saint-Antoine, Sorbonne Université, Université de Bordeaux, Bordeaux Imaging Center, Institut de Génétique Moléculaire de Montpellier
Language: English
Subfield: Biophysics
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,490
OpenAlex ID: W7140166704