Publications

Unai Elordi, Luis Unzueta, Ignacio Arganda-Carreras, and Oihana Otaegui. How Can Deep Neural Networks Be Generated Efficiently for Devices with Limited Resources?. In International Conference on Articulated Motion and Deformable Objects, pp. 24-33. Lecture Notes in Computer Science, vol 10945. Springer, Cham, 2018.
Nerea Aranjuelo, Luis Unzueta, Ignacio Arganda-Carreras, and Oihana Otaegui. Multimodal Deep Learning for Advanced Driving Systems. In International Conference on Articulated Motion and Deformable Objects, pp. 95-105. Lecture Notes in Computer Science, vol 10945. Springer, Cham, 2018.
Ignacio Arganda-Carreras, Tudor Manoliu, Nicolas Mazuras, Florian Schulze, Juan E. Iglesias, Katja Bühler, Arnim Jenett, François Rouyer, and Philippe Andrey. A Statistically Representative Atlas for Mapping Neuronal Circuits in the Drosophila Adult Brain. Frontiers in neuroinformatics 12 (2018): 13.
Ignacio Arganda-Carreras, Verena Kaynig, Curtis Rueden, Kevin W Eliceiri, Johannes Schindelin, Albert Cardona, H Sebastian Seung. Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification. Bioinformatics 2017; 33 (15): 2424-2426. doi:10.1093/bioinformatics/btx180
Ignacio Arganda-Carreras, Philippe Andrey. Designing Image Analysis Pipelines in Light Microscopy: A Rational Approach. Designing Image Analysis Pipelines in Light Microscopy: A Rational Approach. Light Microscopy: Methods and Protocols, 185-207, 2017.
Fadi Dornaika, Ammar Assoum, Abdelmalik Moujahid, Ignacio Arganda-Carreras. An Empirical Study of Global Descriptors for Image-based Localization in Dense Urban Scenes. International Journal of Sensors Wireless Communications and Control, Volume 6, Number 3, December 2016, pp. 142-152(11).
David Legland, Ignacio Arganda-Carreras, Philippe Andrey. MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ. Bioinformatics 2016; 32 (22): 3532-3534. doi: 10.1093/bioinformatics/btw413
Ignacio Arganda-Carreras, Srinivas C. Turaga, Daniel R. Berger, Dan Ciresan, Alessandro Giusti, Luca M. Gambardella, Jürgen Schmidhuber, Dmtry Laptev, Sarversh Dwivedi, Joachim M. Buhmann, Ting Liu, Mojtaba Seyedhosseini, Tolga Tasdizen, Lee Kamentsky, Radim Burget, Vaclav Uher, Xiao Tan, Chanming Sun, Tuan D. Pham, Eran Bas, Mustafa G. Uzunbas, Albert Cardona, Johannes Schindelin, and H. Sebastian Seung. Crowdsourcing the creation of image segmentation algorithms for connectomics. Frontiers in Neuroanatomy, vol. 9, no. 142, 2015.
Yongsoo Kim, Kannan Umadevi Venkataraju, Kith Pradhan, Carolin Mende, Julian Taranda, Srinivas C Turaga, Ignacio Arganda-Carreras, Lydia Ng, Michael J Hawrylycz, Kathleen S Rockland, H Sebastian Seung, Pavel Osten. Mapping Social Behavior-Induced Brain Activation at Cellular Resolution in the Mouse. Cell reports 10 (2), 292-305, 2015.
Javier Cabrera, Fernando E Díaz‐Manzano, Marta Barcala, Ignacio Arganda‐Carreras, Janice Almeida‐Engler, Gilbert Engler, Carmen Fenoll, Carolina Escobar. Phenotyping nematode feeding sites: three‐dimensional reconstruction and volumetric measurements of giant cells induced by root‐knot nematodes in Arabidopsis. New Phytologist, 206 (2), 868-880, 2015.
Axel Poulet, Ignacio Arganda-Carreras, David Legland, Aline V Probst, Philippe Andrey, Christophe Tatout. NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei. Bioinformatics, 31 (7), 1144-1146, 2014.
Nobuhiko Miyasaka, Ignacio Arganda-Carreras, Noriko Wakisaka, Miwa Masuda, Uygar Sümbül, H. Sebastian Seung, and Yoshihiro Yoshihara. Olfactory projectome in the zebrafish forebrain revealed by genetic single-neuron labelling. Nature Communications, 5, 2014.
Jaza Gul-Mohammed, Ignacio Arganda-Carreras, Philippe Andrey, Vincent Galy, and Thomas Boudier. A generic classification-based method for segmentation of nuclei in 3d images of early embryos. BMC bioinformatics, 15(1):9, 2014.
Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid, Jean-Yves Tinevez, Daniel James White, Volker Hartenstein, Kevin Eliceiri, Pavel Tomancak, and Albert Cardona. Fiji: an open-source platform for biological-image analysis. Nature Methods, 9:676–682, June 2012.
Timothy Ragan, Lolahon R. Kadiri, Kannan Umadevi Venkataraju, Karsten Bahlmann, Julian Taranda, Ignacio Arganda-Carreras, Jason Sutin, H. Sebastian Seung, and Pavel Osten. Serial two-photon tomography: an automated method for ex-vivo mouse brain imaging. Nature Methods, 9(3):252–258, January 2012.
Albert Cardona, Stephan Saalfeld, Johannes Schindelin, Ignacio Arganda-Carreras, Stephan Preibisch, Mark Longair, Pavel Tomancak, Volker Hartenstein, and Rodney J. Douglas. TrakEM2: software for neural circuit reconstruction. PLoS ONE, 7(6):e38011, 06 2012.
Michael Doube, Michal M. Klosowski, Ignacio Arganda-Carreras, Fabrice P. Cordelieres, Robert P. Dougherty, Jonathan S. Jackson, Benjamin Schmid, John R. Hutchinson, and Sandra J. Shefelbine. BoneJ: Free and extensible bone image analysis in ImageJ. BONE, 47(6):1076–1079, December 2010.
Albert Cardona, Stephan Saalfeld, Ignacio Arganda-Carreras, Wayne Pereanu, Johannes Schindelin, and Volker Hartenstein. Identifying neuronal lineages of Drosophila by sequence analysis of Axon Tracts. Journal of Neuroscience, 30(22):7538–7553, June 2 2010.
Ignacio Arganda-Carreras, Carlos O. S. Sorzano, Philippe Thévenaz, Arrate Muñoz-Barrutia, Jan Kybic, Roberto Marabini, Jose Maria Carazo, and Carlos Ortiz-de-Solorzano. Non-rigid consistent registration of 2D image sequences. Physics in Medicine and Biology, 55(20):6215, 2010.
Ignacio Arganda-Carreras, Rodrigo Fernandez-Gonzalez, Arrate Muñoz Barrutia, and Carlos Ortiz-de-Solorzano. 3D reconstruction of histological sections: Application to mammary gland tissue. Microscopy Research and Technique, 73(11):1019–1029, October 2010.
Carlos O. S. Sorzano, Ignacio Arganda-Carreras, Philippe Thévenaz, Ana Beloso, Gracia Morales, Israel Valdes, Carmen Perez-Garcia, Carmen Castillo, Elisa Garrido, and Michael Unser. Elastic image registration of 2D gels for differential and repeatability studies. Proteomics, 8:62–65, 2008.
Ignacio Arganda-Carreras, Carlos O. S. Sorzano, Roberto Marabini, Jose-Maria Carazo, Carlos Ortiz-de-Solorzano, and Jan Kybic. Consistent and elastic registration of histological sections using vector-spline regularization. In Computer Vision Approaches to Medical Image Analysis, volume 4241 of Lecture Notes in Computer Science, pages 85–95. Springer Berlin/Heidelberg, May 2006.

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