BioImage Analysis and Computer Vision

Group leader
Ignacio Arganda-Carreras
Address

Biofisika Institute (CSIC-UPV/EHU)
Science Park of the UPV/EHU
Barrio Sarriena s/n. 48940 Leioa, Bizkaia (Spain)

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Research goal
Our lab specializes in advancing computer vision and bioimage analysis for microscopy data. We develop state-of-the-art algorithms to analyze complex biological structures in 2D and 3D, aiming to uncover the intricacies of cellular and molecular interactions. Through interdisciplinary collaboration, we contribute to a quantitative understanding of cellular dynamics, leveraging computational methods to enhance insights into fundamental biological processes.
Group members
DISTINGUISHED UNIVERSITY RESEARCHER / IKERBASQUE RESEARCH ASSOCIATE
PhD Student
Publications

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Carnevali D, Zhong L, González-Almela E, Viana C, Rotkevich M, Wang A, Franco-Barranco D, Gonzalez-Marfil A, Neguembor MV, Castells-Garcia A, Arganda-Carreras I, Cosma MP

A deep learning method that identifies cellular heterogeneity using nanoscale nuclear features
Nat Mach Intell (2024)
doi: 10.1038/s42256-024-00883-x

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Hidalgo-Cenalmor I, Pylvänäinen JW, G Ferreira M, Russell CT, Saguy A, Arganda-Carreras I, Shechtman Y; AI4Life Horizon Europe Program Consortium; Jacquemet G, Henriques R, Gómez-de-Mariscal E

DL4MicEverywhere: deep learning for microscopy made flexible, shareable and reproducible
Nat Methods. 2024 Jun;21(6):925-927
doi: 10.1038/s41592-024-02295-6

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Núñez-Marcos A, Arganda-Carreras I

Transformer-based fall detection in videos
Engineering Applications of Artificial Intelligence Volume 132, June 2024, 107937
DOI: 10.1016/j.engappai.2024.107937

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Abou Ali M, Dornaika F, Arganda-Carreras I

Blood Cell Revolution: Unveiling 11 Distinct Types with ‘Naturalize’ Augmentation
Algorithms. 2023; 16(12):562
DOI: 10.3390/a16120562

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Abou Ali M, Dornaika F, Arganda-Carreras I

White Blood Cell Classification: Convolutional Neural Network (CNN) and Vision Transformer (ViT) under Medical Microscope
Algorithms. 2023; 16(11):525
DOI: 10.3390/a16110525

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Franco-Barranco D, Lin Z, Jang WD, Wang X, Shen Q, Yin W, Fan Y, Li M, Chen C, Xiong Z, Xin R, Liu H, Chen H, Li Z, Zhao J, Chen X, Pape C, Conrad R, Nightingale L, de Folter J, Jones ML, Liu Y, Ziaei D, Huschauer S, Arganda-Carreras I, Pfister H, Wei D

Current Progress and Challenges in Large-Scale 3D Mitochondria Instance Segmentation
IEEE Trans Med Imaging. 2023 Dec;42(12):3956-3971
doi: 10.1109/TMI.2023.3320497

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Andrés-San Román JA, Gordillo-Vázquez C, Franco-Barranco D, Morato L, Fernández-Espartero CH, Baonza G, Tagua A, Vicente-Munuera P, Palacios AM, Gavilán MP, Martín-Belmonte F, Annese V, Gómez-Gálvez P, Arganda-Carreras I, Escudero LM

CartoCell, a high-content pipeline for 3D image analysis, unveils cell morphology patterns in epithelia
Cell Rep Methods. 2023 Oct 23;3(10):100597
doi: 10.1016/j.crmeth.2023.100597