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Book Chapter
Kreshuk A, Funke J, Cardona A, Hamprecht FA.  2015.  Who is talking to whom: Synaptic partner detection in anisotropic volumes of insect brain.. Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2015. :661-8.
Conference Paper
Funke J, Andres B, Hamprecht F, Cardona A, Cook M.  2012.  Efficient automatic 3D-reconstruction of branching neurons from EM data.. Computer Vision and Pattern Recognition (CVPR), 2012 IEEE Conference on.
Journal Article
Saalfeld S, Cardona A, Hartenstein V, Tomancak P..  2010.  As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets.. Bioinformatics. 26(12):i57-63.
MacNamee SE, Liu KE, Gerhard S, Tran CT, Fetter RD, Cardona A, Tolbert LP, Oland LA.  2016.  Astrocytic glutamate transport regulates a Drosophila CNS synapse that lacks astrocyte ensheathment.. The Journal of Comparative Neurology. 524(10):1979-98.
Hörl D, Rusak FRojas, Preusser F, Tillberg P, Randel N, Chhetri RK, Cardona A, Keller PJ, Harz H, Leonhardt H et al..  2019.  BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples.. Nature Methods. 16(9):870-74.
Saalfeld S, Cardona A, Hartenstein V, Tomancak P.  2009.  CATMAID: collaborative annotation toolkit for massive amounts of image data.. Bioinformatics. 25(15):1984-6.
Fushiki A, Zwart MF, Kohsaka H, Fetter RD, Cardona A, Nose A.  2016.  A circuit mechanism for the propagation of waves of muscle contraction in Drosophila.. eLife. 5
Eschbach C, Fushiki A, Winding M, Afonso B, Andrade IV, Cocanougher BT, Eichler K, Gepner R, Si G, Valdes-Aleman J et al..  2021.  Circuits for integrating learned and innate valences in the insect brain.. eLife. 10
Valdes-Aleman J, Fetter RD, Sales EC, Heckman EL, Venkatasubramanian L, Doe CQ, Landgraf M, Cardona A, Zlatic M.  2021.  Comparative Connectomics Reveals How Partner Identity, Location, and Activity Specify Synaptic Connectivity in Drosophila.. Neuron. 109(1):105-22.
Cocanougher BT, Wittenbach JD, Long XSalina, Kohn AB, Norekian TP, Yan J, Colonell J, Masson J-B, Truman JW, Cardona A et al..  2020.  Comparative single-cell transcriptomics of complete insect nervous systems. bioRxiv.
Jovanic T, Schneider-Mizell CM, Shao M, Masson J-B, Denisov G, Fetter RD, Mensh BD, Truman JW, Cardona A, Zlatic M.  2016.  Competitive disinhibition mediates behavioral choice and sequences in Drosophila.. Cell. 167(3):858-70.
Eichler K, Li F, Litwin-Kumar A, Park Y, Andrade I, Schneider-Mizell CM, Saumweber T, Huser A, Eschbach C, Gerber B et al..  2017.  The complete connectome of a learning and memory centre in an insect brain.. Nature. 548(7666):175-182.
Gerhard S, Andrade I, Fetter RD, Cardona A, Schneider-Mizell CM.  2017.  Conserved neural circuit structure across Drosophila larva development revealed by comparative connectomics.. eLife. 6:e29089.
Miroschnikow A, Schlegel P, Schoofs A, Hueckesfeld S, Li F, Schneider-Mizell CM, Fetter RD, Truman JW, Cardona A, Pankratz MJ.  2018.  Convergence of monosynaptic and polysynaptic sensory paths onto common motor outputs in a feeding connectome.. eLife. 7
Imura E, Shimada-Niwa Y, Nishimura T, Hückesfeld S, Schlegel P, Ohhara Y, Kondo S, Tanimoto H, Cardona A, Pankratz MJ et al..  2020.  The corazonin-PTTH neuronal axis controls systemic body growth by regulating basal ecdysteroid biosynthesis in Drosophila melanogaster.. Current Biology. 30(11):2156-65.
Cardona A, Tomancak P.  2012.  Current challenges in open-source bioimage informatics.. Nature Methods. 9(7):661-5.
Mark B, Lai S-L, Zarin AArzan, Manning L, Pollington HQ, Litwin-Kumar A, Cardona A, Truman JW, Doe CQ.  2021.  A developmental framework linking neurogenesis and circuit formation in the Drosophila CNS.. eLife. 10
Andrade IV, Riebli N, Nguyen B-CM, Omoto JJ, Cardona A, Hartenstein V.  2019.  Developmentally arrested precursors of pontine neurons establish an embryonic blueprint of the Drosophila central complex.. Current Biology : CB. 29(3):412-25.
Takagi S, Cocanougher BThomas, Niki S, Miyamoto D, Kohsaka H, Kazama H, Fetter RDoty, Truman JWilliam, Zlatic M, Cardona A et al..  2017.  Divergent connectivity of homologous command-like neurons mediates segment-specific touch responses in Drosophila.. Neuron. 96(6):1373-87.
Sprecher SG, Cardona A, Hartenstein V..  2011.  The Drosophila larval visual system: high-resolution analysis of a simple visual neuropil.. Developmental Biology. 358(1):33-43.
Pogodalla N, Kranenburg H, Rey S, Rodrigues S, Cardona A, Klämbt C.  2021.  Drosophila ß-Spectrin is required in polarized ensheathing glia that form a diffusion-barrier around the neuropil.. Nature Communications. 12(1):6357.
Schröter C, Herrgen L, Cardona A, Brouhard GJ, Feldman B, Oates AC.  2008.  Dynamics of zebrafish somitogenesis.. Developmental Dynamics. 237(3):545-53.
Cardona A, Hartenstein V, Romero R.  2006.  Early embryogenesis of planaria: a cryptic larva feeding on maternal resources.. Development Genes & Evolution. 216(11):667-81.
Saalfeld S, Fetter RD, Cardona A, Tomancak P..  2012.  Elastic volume reconstruction from series of ultra-thin microscopy sections.. Nature Methods. 9(7):717-20.
Cardona A, Hartenstein V, Romero R.  2005.  The embryonic development of the triclad Schmidtea polychroa.. Development Genes & Evolution. 215(3):109-31.