Publications

If you use CATMAID, please cite the following papers:

• Casey M. Schneider-Mizell, Stephan Gerhard, Mark Longair, Tom Kazimiers, Feng Li, Maarten F. Zwart, Andrew Champion, Frank M. Midgley, Richard D. Fetter, Stephan Saalfeld, Albert Cardona. Quantitative neuroanatomy for connectomics in Drosophila, eLife, 2016.

• Stephan Saalfeld, Albert Cardona, Volker Hartenstein, Pavel Tomančák. CATMAID: collaborative annotation toolkit for massive amounts of image data, Bioinformatics, 2009.

A working CATMAID instance often contains a mixture of published and unpublished data. We recommend that you index published data using annotations:

• Annotate neurons and other objects with the citation or DOI (e.g. Ohyama, Schneider-Mizell et al. 2016 or doi:10.1038/nature14297)

• Annotate all publication-related annotations in your instance with the same meta-annotation, e.g. publications (or papers)

This will make data retrieval much easier for the next person who needs it (who may be you!).

If your group uses CATMAID regularly, please get in touch so that you can be added to the Who uses it? page.

Publications using CATMAID

The following publications used CATMAID for neural circuit reconstruction or other tasks. Please get in touch with us if your publication is missing.

2021

• Marcel Ethan Sayre, Rachel Templin, Johanna Chavez, Julian Kempenaers, Stanley Heinze. A projectome of the bumblebee central complex, eLife, 2021

2020

• Claire Eschbach, Akira Fushiki, Michael Winding, Casey M. Schneider-Mizell, Mei Shao, Rebecca Arruda, Katharina Eichler, Javier Valdes-Aleman, Tomoko Ohyama, Andreas S. Thum, Bertram Gerber, Richard D. Fetter, James W. Truman, Ashok Litwin-Kumar, Albert Cardona & Marta Zlatic. Recurrent architecture for adaptive regulation of learning in the insect brain, Nature Neuroscience, 2020.

• Fei Wang, Kaiyu Wang, Nora Forknall, Christopher Patrick, Tansy Yang, Ruchi Parekh, Davi Bock, Barry J. Dickson. Neural circuitry linking mating and egg laying in Drosophila females, Nature, 2020.

• Elizabeth C. Marin, Laurin Büld, Maria Theiss, Tatevik Sarkissian, Ruairí J.V. Roberts, Robert Turnbull, Imaan F.M. Tamimi, Markus W. Pleijzier, Willem J. Laursen, Nik Drummond, Philipp Schlegel, Alexander S. Bates, Feng Li, Matthias Landgraf, Marta Costa, Davi D. Bock, Paul A. Garrity, Gregory S.X.E. Jefferis. Connectomics Analysis Reveals First-, Second-, and Third-Order Thermosensory and Hygrosensory Neurons in the Adult Drosophila Brain, Cell Current Biology, 2020.

• Nils Otto, Markus W. Pleijzier, Isabel C. Morgan, Amelia J. Edmondson-Stait, Konrad J. Heinz, Ildiko Stark, Georgia Dempsey, Masayoshi Ito, Ishaan Kapoor, Joseph Hsu, Philipp M. Schlegel, Alexander S. Bates, Li Feng, Marta Costa, Kei Ito, Davi D. Bock, Gerald M. Rubin, Gregory S.X.E. Jefferis, Scott Waddell. Input Connectivity Reveals Additional Heterogeneity of Dopaminergic Reinforcement in Drosophila, Cell Current Biology, 2020

• Kaylynn E. Coates, Steven A. Calle-Schuler, Levi M. Helmick, Victoria L. Knotts, Brennah N. Martik, Farzaan Salman, Lauren T. Warner, Sophia V. Valla, Davi D. Bock and Andrew M. Dacks. The Wiring Logic of an Identified Serotonergic Neuron That Spans Sensory Networks, Journal of Neuroscience, 2020

2019

• Jan M. Ache, Jason Polsky, Shada Alghailani, Ruchi Parekh, Patrick Breads, Martin Y. Peek, Davi D. Bock, Catherine R. von Reyn, Gwyneth M. Card. Neural Basis for Looming Size and Velocity Encoding in the Drosophila Giant Fiber Escape Pathway, Cell Current Biology, 2019.

• Tihana Jovanic, Michael Winding, Albert Cardona, James W. Truman, Marc Gershow, Marta Zlatic. Neural Substrates of Drosophila Larval Anemotaxis, Cell Current Biology, 2019.

• Sercan Sayin, Jean-Francois De Backer, K.P. Siju, Marina E. Wosniack, Laurence P. Lewis, Lisa-Marie Frisch, Benedikt Gansen, Philipp Schlegel, Amelia Edmondson-Stait, Nadiya Sharifi, Corey B. Fisher, Steven A. Calle-Schuler, J. Scott Lauritzen, Davi D. Bock, Marta Costa, Gregory S.X.E. Jefferis, Julijana Gjorgjieva, Ilona C. Grunwald Kadow. A Neural Circuit Arbitrates between Persistence and Withdrawal in Hungry Drosophila, Cell Neuron, 2019

2018

• Luis A. Bezares-Calderón, Jürgen Berger, Sanja Jasek, Csaba Verasztó, Sara Mendes, Martin Gühmann, Rodrigo Almeda, Réza Shahidi, Gáspár Jékely. Neural circuitry of a polycystin-mediated hydrodynamic startle response for predator avoidance, eLife, 2018.

• Johannes Felsenberg, Pedro F. Jacob, Thomas Walker, Oliver Barnstedt, Amelia J. Edmondson-Stait, Markus W. Pleijzier, Nils Otto, Philipp Schlegel, Nadiya Sharifi, Emmanuel Perisse, Carlas S. Smith, J. Scott Lauritzen, Marta Costa, Gregory S.X.E. Jefferis, Davi D. Bock, Scott Waddell Integration of Parallel Opposing Memories Underlies Memory Extinction, Cell, 2018

• Michael-John Dolan, Ghislain Belliart-Guérin, Alexander Shakeel Bates, Shahar Frechter, Aurélie Lampin-Saint-Amaux, Yoshinori Aso, Ruairí J.V. Roberts, Philipp Schlegel, Allan Wong, Adnan Hammad, Davi Bock, Gerald M. Rubin, Thomas Preat, Pierre-Yves Plaçais, Gregory S.X.E. Jefferis Communication from Learned to Innate Olfactory Processing Centers Is Required for Memory Retrieval in Drosophila, Neuron, 2018

• Tatsuya C. Murakami, Tomoyuki Mano, Shu Saikawa, Shuhei A. Horiguchi, Daichi Shigeta, Kousuke Baba, Hiroshi Sekiya, Yoshihiro Shimizu, Kenji F. Tanaka, Hiroshi Kiyonari, Masamitsu Iino, Hideki Mochizuki, Kazuki Tainaka & Hiroki R. Ueda. A three-dimensional single-cell-resolution whole-brain atlas using CUBIC-X expansion microscopy and tissue clearing, Nature Neuroscience, 2018.

• Zhihao Zheng, J. Scott Lauritzen, Eric Perlman, Camenzind G. Robinson, Matthew Nichols, Daniel Milkie, Omar Torrens, John Price, Corey, B. Fisher, Nadiya Sharifi, Steven A. Calle-Schuler, Lucia Kmecova, Iqbal J. Ali, Bill Karsh, Eric T. Trautman, John A. Bogovic, Philipp Hanslovsky, Gregory S.X.E. Jefferis, Michael Kazhdan, Khaled Khairy, Stephan Saalfeld, Richard D. Fetter, Davi D. Bock. A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster, Cell, 2018.

2017

• Stephan Gerhard, Ingrid Andrade, Richard D. Fetter, Albert Cardona, Casey M. Schneider-Mizell. Conserved neural circuit structure across Drosophila larva development revealed by comparative connectomics, eLife, 2017.

• Katharina Eichler, Feng Li, Ashok Litwin-Kumar, Youngser Park, Ingrid Andrade, Casey M. Schneider-Mizell, Timo Saumweber, Annina Huser, Claire Eschbach, Bertram Gerber, Richard D. Fetter, James W. Truman, Carey E. Priebe, L. F. Abbott, Andreas S. Thum, Marta Zlatic, Albert Cardona. The complete connectome of a learning and memory centre in an insect brain, Nature, 2017.

• Ivan Larderet, Pauline M. J. Fritsch, Nanae Gendre, G. Larisa Neagu-Maier, Richard D. Fetter, Casey M. Schneider-Mizell, James W. Truman, Marta Zlatic, Albert Cardona, Simon G. Sprecher. Organization of the Drosophila larval visual circuit, eLife, 2017.

• David G. C. Hildebrand, Marcelo Cicconet, Russel M. Torres, Woohyuk Choi, Tran Minh Quan, Jungmin Moon, Arthur W. Wetzel, Andrew S. Champion, Brett J. Graham, Owen Randlett, George S. Plummer, Ruben Portugues, Isaac H. Bianco, Stephan Saalfeld, Alexander D. Baden, Kunal Lillaney, Randal Burns, Joshua T. Vogelstein, Alexander F. Schier, Wei-Chung Allen Lee, Won-Ki Jeong, Jeff W. Lichtman, Florian Engert. Whole-brain serial-section electron microscopy in larval zebrafish, Nature, 2017.

• William F. Tobin, Rachel I. Wilson, Wei-Chung Allen Lee. Wiring variations that enable and constrain neural computation in a sensory microcircuit, eLife, 2017.

• Csaba Verasztó, Nobuo Ueda, Luis A. Bezares-Calderón, Aurora Panzera, Elizabeth A. Williams, Réza Shahidi, Gáspár Jékely. Ciliomotor circuitry underlying whole-body coordination of ciliary activity in the Platynereis larva, eLife, 2017.

• Suguru Takagi, Benjamin T. Cocanougher, Sawako Niki, Dohjin Miyamoto, Hiroshi Kohsaka, Hokto Kazama, Richard D. Fetter, James W. Truman, Marta Zlatic, Albert Cardona, Akinao Nose Divergent connectivity of homologous command-like neurons mediates segment-specific touch responses in Drosophila, Neuron, 2017.

2016

• Tihana Jovanic, Casey M. Schneider-Mizell, Mei Shao, Jean-Baptiste Masson, Gennady Denisov, Richard D. Fetter, Brett D. Mensh, James W. Truman, Albert Cardona, Marta Zlatic. Competitive disinhibition mediates behavioral choice and sequences in Drosophila, Cell, 2016.

• Wei-Chung Allen Lee, Vincent Bonin, Michael Reed, Brett J. Graham, Greg Hood, Katie Glattfelder, R. Clay Reid. Anatomy and function of an excitatory network in the visual cortex, Nature, 2016.

• Matthew E. Berck, Avinash Khandelwal, Lindsey Claus, Luis Hernandez-Nunez, Guangwei Si, Christopher J. Tabone, Feng Li, James W. Truman, Richard D. Fetter, Matthieu Louis, Aravinthan D. T. Samuel, Albert Cardona. The wiring diagram of a glomerular olfactory system, eLife, 2016.

• Akira Fushiki, Maarten F. Zwart, Hiroshi Kohsaka1, Richard D. Fetter, Albert Cardona, Akinao Nose. A circuit mechanism for the propagation of waves of muscle contraction in Drosophila, eLife, 2016.

• Philipp Schlegel, Michael J. Texada, Anton Miroschnikow, Andreas Schoofs, Sebastian Hückesfeld, Marc Peters, Casey M. Schneider-Mizell, Haluk Lacin, Feng Li. Synaptic transmission parallels neuromodulation in a central food-intake circuiti, eLife, 2016

2015

• Tomoko Ohyama, Casey M. Schneider-Mizell, Richard D. Fetter, Javier Valdes Aleman, Romain Franconville, Marta Rivera-Alba, Brett D. Mensh, Kristin M. Branson, Julie H. Simpson, James W. Truman, Albert Cardona, Marta Zlatic. A multilevel multimodal circuit enhances action selection in Drosophila. Nature, 2015.

• Ellie S. Heckscher, Aref Arzan Zarin, Serge Faumont, Matthew Q. Clark, Laurina Manning, Akira Fushiki, Casey M. Schneider-Mizell, Richard D. Fetter, James W. Truman, Maarten F. Zwart, Matthias Landgraf, Albert Cardona, Shawn R. Lockery, Chris Q. Doe. Even-skipped+ interneurons are core components of a sensorimotor circuit that maintains left-right symmetric muscle contraction amplitude, Neuron, 2015.

• Nadine Randel, Réza Shahidi, Csaba Verasztó, Luis A Bezares-Calderón, Steffen Schmidt, Gáspár Jékely. Inter-individual stereotypy of the Platynereis larval visual connectome, eLife, 2015.

• Réza Shahidi, Elizabeth A Williams, Markus Conzelmann, Albina Asadulina, Csaba Verasztó, Sanja Jasek, Luis A Bezares-Calderón, Gáspár Jékely. A serial multiplex immunogold labeling method for identifying peptidergic neurons in connectomes, eLife, 2015

• Sebastian Dunst, Tom Kazimiers, Felix von Zadow, Helena Jambor, Andreas Sagner, Beate Brankatschk, Ali Mahmoud, Stephanie Spannl, Pavel Tomančák, Suzanne Eaton, Marko Brankatschk. Endogenously tagged rab proteins: a resource to study membrane trafficking in Drosophila, Developmental Cell, 2015

• Fernando Amat, Burkhard Höckendorf, Yinan Wan, William C. Lemon, Katie McDole, Philipp J. Keller. Efficient processing and analysis of large-scale light-sheet microscopy data., Nature Protocols, 2015