Publications

Articles in peer-reviewed journals

Albert Cardona. 2013. Towards semi-automatic reconstruction of neural circuits. Neuroinformatics 11(1): 31-3. DOI:10.1007/s12021-012-9166-x. Commentary. PDF
Stephan Saalfeld, Richard Fetter, Albert Cardona, Pavel Tomancak. 2012. Elastic Volume Reconstruction from Series of Ultra-thin Microscopy Sections. Nature Methods doi:10.1038/nmeth.2072. PDF
Albert Cardona and Pavel Tomancak. 2012. Current challenges in open-source bioimage informatics. Nature Methods 9:661-5. Commentary. PDF
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, Albert Cardona. 2012. Fiji - an Open Source platform for biological image analysis. Nature Methods 9:676-82. PDF
Albert Cardona, Stephan Saalfeld, Johannes Schindelin, Ignacio Arganda-Carreras, Stephan Preibisch, Mark Longair, Pavel Tomancak, Volker Hartenstein, Rodney J. Douglas. 2012. TrakEM2 software for neural circuit reconstruction. PLoS ONE 7(6): e38011.
Jan Funke, Bjoern Andres, Fred Hamprecht, Albert Cardona, Matthew Cook. 2012. Efficient Automatic 3D-Reconstruction of Branching Neurons from EM Data. CVPR 2012. [PDF]
Sprecher S, Cardona A, Hartenstein V. 2011. The Drosophila larval visual system: High-resolution analysis of a simple visual neuropil. Developmental Biology. [PDF]
Cardona A, Saalfeld S, Preibisch S, Schmid B, Cheng A, Pulokas J, Tomancak P, Hartenstein V. 2010. An Integrated Micro- and Macroarchitectural Analysis of the Drosophila Brain by Computer-Assisted Serial Section Electron Microscopy. PLoS Biol 8(10): e1000502. doi:10.1371/journal.pbio.1000502.
Bery A, Cardona A, Martinez P, Hartenstein V. 2010. Structure of the central nervous system of a juvenile acoel, Symsagittifera roscoffensis. Dev Genes Evol. 220(3-4):61-76.
Cardona A, Saalfeld S, Arganda I, Pereanu W, Schindelin J, Hartenstein V. 2010. Identifying neuronal lineages of Drosophila by sequence analysis of axon tracts. J Neurosci 30(22):7538-7553. doi:10.1523/JNEUROSCI.0186-10.2010. [PDF]
Saalfeld S, Cardona A, Hartenstein V, Tomancák P. 2010. As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets. Bioinformatics. 2010 Jun 15;26(12):i57-63. [Link]
Schmid B, Schindelin J, Cardona A, Longair M, Heinsenberg M. 2010. A high-level 3D visualization API for Java and ImageJ. BMC Bioinformatics 11:274. doi:10.1186/1471-2105-11-274. [Link]
Cardona A, Saalfeld S, Tomancak T, Hartenstein V. 2009. Drosophila brain development: closing the gap between a macroarchitectural and microarchitectural approach. Cold Spring Harb Symp Quant Biol. sqb.2009.74.037, Dec 22. [PDF]
Cardona A, Larsen C, Hartenstein V. Neuronal fiber tracts connecting the brain and ventral nerve cord of the early Drosophila larva. 2009. J Comp Neurol. 515(4):427-40. DOI: 10.1002/cne.22086 [PDF]
Saalfeld S, Cardona A, Hartenstein V, Tomancak P. CATMAID: Collaborative Annotation Toolkit for Massive Amounts of Image Data. Bioinformatics. 2009 Apr 17. [paper]
Schröter C, Herrgen L, Cardona A, Brouhard GJ, Feldman B, Oates AC. 2008. Dynamics of zebrafish somitogenesis. Dev. Dyn. Feb 8. [PDF]
Morris, J., Cardona, A., de Miguel-Bonet M. del M. and Hartenstein, V. 2007. Neurobiology of the basal platyhelminth Macrostomum lignano: map and digital 3D model of the juvenile brain neuropile. Dev. Genes Evol. 217(8):569-84. [PDF]
Cardona, A., Hartenstein, V., Romero, R. 2006. Early embryogenesis of planaria: a cryptic larva feeding on maternal resources. Dev. Genes Evol. 216: 667-81. [ PDF ]
Cardona, A., Fernández-Rodríguez, J., Solana, J., Romero, R. 2005. An in situ hybridization protocol for planarian embryos: monitoring myosin heavy chain gene expression. Development Genes and Evolution, 215(9):436-42. [PDF]
Cardona, A., Hartenstein, V., Romero, R. 2005. The embryonic development of the triclad Schmidtea polychroa. Development Genes and Evolution 215(3):109-131. [PDF]
Bueno. D., Fernández-Rodríguez J., Cardona, A., Hernández-Hernández, V., Romero, R. 2002. A novel invertebrate trophic factor related to invertebrate neurotrophins is involved in planarian body regional survival and asexual reproduction. Developmental Biology 252: 188-201.

Other publications

"Entendre el genoma: les xarxes booleanes com a model." (Understanding the genome: boolean networks as a model). Omnis Cellula 4 (March 2004). [PDF]

Contributions to conferences, meetings and symposia

Cardona A, Saalfeld S, Tomancak P, Hartenstein V. "TrakEM2: open source software for neuronal reconstruction from large serial section microscopy data." High Resolution Circuits Reconstruction, joint meeting of HHMI Janelia Farm and Max Plank Gesellschaft. September 20-22, 2009.
Cardona, A. "The real neurons: imaging/reconstructing/identifying neurons from serial sections." Neurinformatics 2009, Pilsen, Czech Republic. September 3-6, 2009.
Cardona A, Fetter R, Pereanu W, Zlatic M, Simpson J, and Hartenstein V. "Serial section TEM of a VNC abdominal segment: finding synaptic partners of neurons identified in a behavioral screen." Maggot Meeting, HHMI Janelia Farm. October 20-22, 2008.
Cardona, A. Blender's Game Engine as a Live 3D Simulator for External Programs. Blender Conference 2007. De Zwijger, Amsterdam, 12-14 October 2007. The Netherlands. Workshop.
Cardona, A., Saalfeld, S., Preibisch, S., Tomancak, P. and Hartenstein, V. 2007. Serial section TEM of fly brain. HHMI Janelia Farms Conference on Neural Circuit Reconstruction, Sept. 22-25, 2007. Poster.
Cardona, A. and Hartenstein, V. "Fly Bran Microcircuitry." Neuroanatomy and Stereotypy of the Adult Drosophila Nervous System. HHMI Janelia Farms Conference. March 11-13, 2007. Poster and poster handout.
Cardona, A. and Hartenstein, V. "Drosophila CNS Connectivity. A study of the first instar larva." Neurofly 2007. Leuven, Belgium. Talk slides and poster.
Cardona, A. "3D Modeling Fly Brains: Biologists Use Blender as a Tool." Blender Conference 2006. The Haag, Amsterdam, The Netherlands. Abstract, paper [ PDF ], talk slides and talk video recording.
Cardona, A. Hartenstein, V. and Romero, R. "Early embryonic development of planarians." International Symposium of Flatworm Biology, Innsbruck 2006. Talk slides and Macrostomum brain poster
Cardona, A. "TrakEM2: an ImageJ-based program for morphological data mining and 3D modeling." 1st ImageJ User and Developer Conference, Centre de Recherche Public Henri Tudor, Luxembourg, May 18-19th 2006. Talk slides.
Cardona, A., Fernández-Rodríguez, J., Solana, J., Vila, M., Hartenstein, V., Romero, R. 2005. "Planarian development." Memorial Campos-Ortega, Sevilla (Spain), May 12-16. Poster.
Cardona, A., Fernández-Rodríguez, J., Vila, M., Hernández-Hernández, V., Solana, J., Cuesta, N., Bueno, D., Hartenstein, V., Romero, R. 2003. "Insights into embryonic development of the planarian Schmidtea polychroa." CNRS - Conference Jacques Monod: Form and Function in Development and Disease. La Londe-les-Maures (France). June14-18th, 2003. Poster.

Seminars and courses

"Identifying Drosophila's secondary neuronal lineages by sequence analysis of their projection bundles." Seminar organized by Giorgio Ascoli. Krasnow Institute for Advanced Study, George Mason University, Washington DC.
"INCF Fiji Image Processing School", funded by David Wilshaw (UK INCF node) and Thomas Watchler (Germany INCF node). Plzen, Czech Republic, September 9-12, 2009. Organizer and instructor.
"Neuronal reconstruction of Drosophila larvae central nervous system." Hosted by Nico Beerenwinkel of the Computational Biology Group. Department of Biosystems Science and Engineering, Systems X, ETH Zürich; Basel. May 13th, 2009.
"Identifying Drosophila's secondary neuronal lineages by sequence analysis of their projection bundles." Seminar hosted by Heinrich Reichert, Biozentrum, Nrurobiology, University of Basel. May 12th, 2009.
"Fiji: an overview." EMBL Heildelberg, February 5th, 2009.
"The Drosophila first instar larval brain." EMBL Heidelberg, February 4th, 2009.
"TrakEM2: montage/register/analyze/segment terabytes of images. The Drosophila first instar larval brain." FENS Geneve, July 2008. Session co-chair.
"From micro to nano: mapping neuroanatomical data from confocal imaging to TEM serial sections and back." Seminar hosted by Matthieu Louis at Centre de Regulació Genòmica (CRG) in Barcelona, Spain. 2008
"Neuroanatomy of Drosophila larval brain." Seminar hosted by the Reid (and Lichtman) labs, Harvard, Boston. May 9th, 2008.
"Bioinformatics for neurons. Identifying neurons by sequence analysis of their 3D structure." Image Processing Journal Club hosted by Hanchuan Peng and Gene Myers. April 17th, 2008. Janelia Farm, Washington.
"Fly brain connectivity." Joint Friday Seminar with Pavel and Stephan Saalfeld, from Pavel Tomancak's group at the Max Plank Institute for Molecular Cell Biology and Genetics-CBG. October 19th, 2007. Dresden, Germany.
"Analyzing neuronal structure and connectivity." Leiden University. October 16th, 2007. Leiden, the Netherlands.
"Microcircuitry." Together with Volker Hartenstein. Scripps Institute, January 25th 2007, San Diego.
"Fundamentals of Image Processing." Together with Pavel Tomancak and Andy Oates. December 2006 at the Max Plank Institute for Molecular Cell Biology and Genetics, Dresden. Course paper [ PDF ] and presentation slides
"ImageJ." November 2006 at the Max Plank Institute for Molecular Cell Biology and Genetics. Slides of the talk.
"Embryonic development of planarians" at Nico Michiel's lab, Tuebingen, November 15-18th 2006. Slides of the talk.

PhD Thesis

"The embryonic development of the triclad Schmidtea polychroa."
Defended July 19th, 2005, at the University of Barcelona, Spain. Directed by Prof. Rafael Romero.
Available in printing quality [ PDF ]; also the public defense slides.