Daniel Franco-Barranco

HPC Resources Technician and PhD Candidate

About Me

Hi, my name’s Daniel and I work as half-time HPC Resources Technician at Donostia International Physics Center (DIPC), being part of the management and configuration of the biggest cluster of the Basque Country. The other half of my workday I’m a PhD Candidate at the University of the Basque Country, together with the DIPC, advised by Prof. Ignacio Arganda-Carreras and Prof. Arrate Muñoz-Barrutia.

My general research area is in Biomedical image processing and Computer Vision, focused in the design and development of novel Deep Learning solutions for the segmentation of organelles in large Electron microscope images and across microscope types and modalities.


2019 - present

PhD Candidate at University of the Basque Country (UPV/EHU)

2015 - present

HPC Resources Technician at Donostia International Physics Center (DIPC)

2022 (6 months)

PhD Intern at Harvard, advised by Prof. Donglai Wei and Prof. Hanspeter Pfister

2018 - 2019 (1 year)

Master’s degree in Computational Engineering and Intelligent Systems

2011 - 2015 (4 years)

Bachelor’s degree in Computer Engineering

2014 (6 months)

Company practices at Donostia International Physics Center (DIPC)




Current Progress and Challenges in Large-scale 3D Mitochondria Instance Segmentation

Daniel Franco-Barranco, Zudi Lin, Won-Dong Jang, Xueying Wang, Qijia Shen, Wenjie Yin, Yutian Fan, Mingxing Li, Chang Chen, Zhiwei Xiong, Rui Xin, Hao Liu, Huai Chen, Zhili Li, Jie Zhao, Xuejin Chen, Constantin Pape, Ryan Conrad, Jozefus De Folter, Luke Nightingale, Martin Jones, Yanling Liu, Dorsa Ziaei, Stephan Huschauer, Ignacio Arganda-Carreras, Hanspeter Pfister, Donglai Wei

TechRxiv BibTeX PDF Code



CartoCell, a high-throughput pipeline for accurate 3D image analysis, unveils cell morphology patterns in epithelial cysts

Jesús A. Andrés-San Román, Carmen Gordillo-Vazquez, Daniel Franco-Barranco, Laura Morato, Antonio Tagua, Pablo Vicente-Munuera, Ana M. Palacios, Maria P. Gavilan, Valentina Annese, Pedro Gómez-Gálvez, Ignacio Arganda-Carreras, Luis M. Escudero

bioRxiv BibTeX PDF Code



Deep learning based domain adaptation for mitochondria segmentation on EM volumes

Daniel Franco-Barranco, Julio Pastor-Tronch, Aitor González-Marfil, Arrate Muñoz-Barrutia, Ignacio Arganda-Carreras

CMPB arXiv BibTeX PDF Sup. material Code


Cell Systems

A quantitative biophysical principle to explain the 3D cellular connectivity in curved epithelia

Pedro Gómez-Gálvez, Pablo Vicente-Munuera, Samira Anbari, Antonio Tagua, Carmen Gordillo-Vázquez, Jesús A. Andrés-San Román, Daniel Franco-Barranco, Ana M. Palacios, Antonio Velasco, Carlos Capitán-Agudo, Clara Grima, Valentina Annese, Ignacio Arganda-Carreras, Rafael Robles, Alberto Márquez, Javier Buceta, Luis M. Escudero

Cell Systems bioRxiv BibTeX PDF Code


Computer Methods and Programs
in Biomedicine

Building a Bioimage Analysis Workflow using Deep Learning

Estibaliz Gómez-de-Mariscal, Daniel Franco-Barranco, Arrate Muñoz-Barrutia, Ignacio Arganda-Carreras

Book Github



Stable deep neural network architectures for mitochondria segmentation on electron microscopy volumes

Daniel Franco-Barranco, Arrate Muñoz-Barrutia, Ignacio Arganda-Carreras

Neuroinformatics arXiv BibTeX PDF Code



MitoEM Dataset: Large-scale 3D Mitochondria Instance Segmentation from EM Images

Donglai Wei, Zudi Lin, Daniel Franco-Barranco, Nils Wendt, Xingyu Liu, Wenjie Yin, Xin Huang, Aarush Gupta, Won-Dong Jang, Xueying Wang, Ignacio Arganda-Carreras, Jeff W. Lichtman, Hanspeter Pfister

PDF BibTeX Code