MitoEM Dataset: Large-scale 3D Mitochondria Instance Segmentation from EM Images
Wei, Donglai, Lin, Zudi, Franco-Barranco, Daniel, Wendt, Nils, Liu, Xingyu, Yin, Wenjie, Huang, Xin, Gupta, Aarush, Jang, Won-Dong, Wang, Xueying, Arganda-Carreras, Ignacio, Lichtman, Jeff W, Pfister, Hanspeter
Published in Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention (2020)
Published in Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention (2020)
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Journal Article
CartoCell, a high-content pipeline for 3D image analysis, unveils cell morphology patterns in epithelia
Andrés-San Román, Jesús A., Gordillo-Vázquez, Carmen, Franco-Barranco, Daniel, Morato, Laura, Fernández-Espartero, Cecilia H., Baonza, Gabriel, Tagua, Antonio, Vicente-Munuera, Pablo, Palacios, Ana M., Gavilán, María P., Martín-Belmonte, Fernando, Annese, Valentina, Gómez-Gálvez, Pedro, Arganda-Carreras, Ignacio, Escudero, Luis M.
Published in Cell reports methods (23.10.2023)
Published in Cell reports methods (23.10.2023)
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Journal Article
Deep learning based domain adaptation for mitochondria segmentation on EM volumes
Franco-Barranco, Daniel, Pastor-Tronch, Julio, González-Marfil, Aitor, Muñoz-Barrutia, Arrate, Arganda-Carreras, Ignacio
Published in Computer methods and programs in biomedicine (01.07.2022)
Published in Computer methods and programs in biomedicine (01.07.2022)
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Journal Article
Self-supervised Vision Transformers for image-to-image labeling: a BiaPy solution to the LightMyCells Challenge
Franco-Barranco, Daniel, Gonzalez-Marfil, Aitor, Arganda-Carreras, Ignacio
Published in 2024 IEEE International Symposium on Biomedical Imaging (ISBI) (27.05.2024)
Published in 2024 IEEE International Symposium on Biomedical Imaging (ISBI) (27.05.2024)
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Conference Proceeding
Characterizing structure formation through instance segmentation
López-Cano, Daniel, Stücker, Jens, Pellejero Ibañez, Marcos, Angulo, Raúl E., Franco-Barranco, Daniel
Published in Astronomy and astrophysics (Berlin) (01.05.2024)
Published in Astronomy and astrophysics (Berlin) (01.05.2024)
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Journal Article
Current Progress and Challenges in Large-Scale 3D Mitochondria Instance Segmentation
Franco-Barranco, Daniel, Lin, Zudi, Jang, Won-Dong, Wang, Xueying, Shen, Qijia, Yin, Wenjie, Fan, Yutian, Li, Mingxing, Chen, Chang, Xiong, Zhiwei, Xin, Rui, Liu, Hao, Chen, Huai, Li, Zhili, Zhao, Jie, Chen, Xuejin, Pape, Constantin, Conrad, Ryan, Nightingale, Luke, de Folter, Joost, Jones, Martin L., Liu, Yanling, Ziaei, Dorsa, Huschauer, Stephan, Arganda-Carreras, Ignacio, Pfister, Hanspeter, Wei, Donglai
Published in IEEE transactions on medical imaging (01.12.2023)
Published in IEEE transactions on medical imaging (01.12.2023)
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Journal Article
Modeling Wound Healing Using Vector Quantized Variational Autoencoders and Transformers
Backova, Lenka, Bengoetxea, Guillermo, Rogalla, Svana, Franco-Barranco, Daniel, Solon, Jerome, Arganda-Carreras, Ignacio
Published in 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI) (18.04.2023)
Published in 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI) (18.04.2023)
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Conference Proceeding
A deep learning method that identifies cellular heterogeneity using nanoscale nuclear features
Carnevali, Davide, Zhong, Limei, González-Almela, Esther, Viana, Carlotta, Rotkevich, Mikhail, Wang, Aiping, Franco-Barranco, Daniel, Gonzalez-Marfil, Aitor, Neguembor, Maria Victoria, Castells-Garcia, Alvaro, Arganda-Carreras, Ignacio, Cosma, Maria Pia
Published in Nature machine intelligence (2024)
Published in Nature machine intelligence (2024)
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Journal Article
BiaPy: a ready-to-use library for Bioimage Analysis Pipelines
Franco-Barranco, Daniel, Andres-San Roman, Jesus A., Gomez-Galvez, Pedro, Escudero, Luis M., Munoz-Barrutia, Arrate, Arganda-Carreras, Ignacio
Published in 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI) (18.04.2023)
Published in 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI) (18.04.2023)
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Conference Proceeding
A quantitative biophysical principle to explain the 3D cellular connectivity in curved epithelia
Gómez-Gálvez, Pedro, Vicente-Munuera, Pablo, Anbari, Samira, Tagua, Antonio, Gordillo-Vázquez, Carmen, Andrés-San Román, Jesús A., Franco-Barranco, Daniel, Palacios, Ana M., Velasco, Antonio, Capitán-Agudo, Carlos, Grima, Clara, Annese, Valentina, Arganda-Carreras, Ignacio, Robles, Rafael, Márquez, Alberto, Buceta, Javier, Escudero, Luis M.
Published in Cell systems (17.08.2022)
Published in Cell systems (17.08.2022)
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Journal Article
Characterizing Structure Formation through Instance Segmentation
López-Cano, Daniel, Stücker, Jens, Ibañez, Marcos Pellejero, Angulo, Raúl E, Franco-Barranco, Daniel
Year of Publication 20.11.2023
Year of Publication 20.11.2023
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Journal Article
Stable deep neural network architectures for mitochondria segmentation on electron microscopy volumes
Franco-Barranco, Daniel, Muñoz-Barrutia, Arrate, Arganda-Carreras, Ignacio
Year of Publication 08.04.2021
Year of Publication 08.04.2021
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Journal Article
Deep learning based domain adaptation for mitochondria segmentation on EM volumes
Franco-Barranco, Daniel, Pastor-Tronch, Julio, Gonzalez-Marfil, Aitor, Muñoz-Barrutia, Arrate, Arganda-Carreras, Ignacio
Year of Publication 22.02.2022
Year of Publication 22.02.2022
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Journal Article
BiaPy: A unified framework for versatile bioimage analysis with deep learning
Franco-Barranco, Daniel, Andres-San Roman, Jesus Angel, Hidalgo-Cenalmor, Ivan, Backova, Lenka, Gonzalez-Marfil, Aitor, Clement Caporal, Chessel, Anatole, Gomez-Galvez, Pedro, Escudero, Luis M, Donglai Wei, Munoz-Barrutia, Arrate, Arganda-Carreras, Ignacio
Published in bioRxiv (05.02.2024)
Published in bioRxiv (05.02.2024)
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Paper
CartoCell, a high-throughput pipeline for accurate 3D image analysis, unveils cell morphology patterns in epithelial cysts
Andres-San Roman, Jesus A, Gordillo-Vazquez, Carmen, Franco-Barranco, Daniel, Morato, Laura, Tagua, Antonio, Vicente-Munuera, Pablo, Palacios, Ana M, Gavilan, Maria P, Annese, Valentina, Gomez-Galvez, Pedro, Arganda-Carreras, Ignacio, Escudero, Luis M
Published in bioRxiv (06.01.2023)
Published in bioRxiv (06.01.2023)
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Paper
A quantitative biophysical principle to explain the 3D cellular connectivity in curved epithelia
Gomez-Galvez, Pedro, Vicente-Munuera, Pablo, Anbari, Samira, Tagua, Antonio, Gordillo, Carmen, Andres-San Roman, Jesus A, Franco-Barranco, Daniel, Palacios, Ana Maria, Velasco, Antonio, Capitan-Agudo, Carlos, Grima, Clara, Annese, Valentina, Arganda-Carreras, Ignacio, Robles, Rafael, Marquez, Alberto, Buceta, Javier, Escudero, Luis M
Published in bioRxiv (13.05.2022)
Published in bioRxiv (13.05.2022)
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Paper