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Department of Zoology



I am a Senior Research Associate and Project Lead for the Drosophila Connectomics group in the Department of Zoology at the University of Cambridge, since November 2016.

This project is a consortium of 2 groups in the UK (Cambridge, Oxford) and 2 in the US (Janelia Research Campus and University of Vermont) and funded by the Wellcome Trust. The Cambridge group is lead by Greg Jefferis and Matthias Landgraf. The project aims to describe the circuits involved in innate and learning olfactory behaviour using the first electron-microscopy whole adult brain dataset generated at Janelia Research Campus by Davi Bock.

I have been interested in pursuing neuroscience research since my undergraduate degree in Biology at the University of Lisbon, Portugal. After completing a MSc Neuroscience at UCL with Jon Clarke, using real-time imaging to analyse zebrafish neurulation, I moved to Cambridge for a PhD. Working in the lab of Pat Simpson, I focused on describing the pathways responsible for the patterning of thoracic bristles in different species of flies.

In 2011, looking to contribute to community resources, I started my first postdoc with the Virtual Fly Brain project (VFB) and later on, also joined FlyBase. Both projects are large research collaborations that collect and integrate Drosophila data (neuronal or genetic, respectively), making it available to the community via a web-based resource. I focused on image analysis and neuroanatomy curation, and in a collaboration with Greg Jefferis (MRC-LMB), developed the neuronal similarity algorithm NBLAST, now used by various groups. I am currently a Co-Investigator on VFB.

I am also a Postdoctoral Research Associate at Lucy Cavendish College.


Key publications: 


Other publications: 
  • Scheffer, Louis K and Xu, C Shan and Januszewski, Michal and Lu, Zhiyuan and Takemura, Shin-ya and Hayworth, Kenneth J and Huang, Gary B and Shinomiya, Kazunori and Maitlin-Shepard, Jeremy and Berg, Stuart and Clements, Jody and Hubbard, Philip M and Katz, William T and Umayam, Lowell and Zhao, Ting and Ackerman, David and Blakely, Tim and Bogovic, John and Dolafi, Tom and Kainmueller, Dagmar and Kawase, Takashi and Khairy, Khaled A and Leavitt, Laramie and Li, Peter H and Lindsey, Larry and Neubarth, Nicole and Olbris, Donald J and Otsuna, Hideo and Trautman, Eric T and Ito, Masayoshi and Bates, Alexander S and Goldammer, Jens and Wolff, Tanya and Svirskas, Robert and Schlegel, Philipp and Neace, Erika and Knecht, Christopher J and Alvarado, Chelsea X and Bailey, Dennis A and Ballinger, Samantha and Borycz, Jolanta A and Canino, Brandon S and Cheatham, Natasha and Cook, Michael and Dreher, Marisa and Duclos, Octave and Eubanks, Bryon and Fairbanks, Kelli and Finley, Samantha and Forknall, Nora and Francis, Audrey and Hopkins, Gary Patrick and Joyce, Emily M and Kim, SungJin and Kirk, Nicole A. and Kovalyak, Julie and Lauchie, Shirley and Lohff, Alanna and Maldonado, Charli and Manley, Emily A and McLin, Sari and Mooney, Caroline and Ndama, Miatta and Ogundeyi, Omotara and Okeoma, Nneoma and Ordish, Christopher and Padilla, Nicholas and Patrick, Christopher M and Paterson, Tyler and Phillips, Elliott E. and Phillips, Emily M. and Rampally, Neha and Ribeiro, Caitlin and Robertson, Madelaine K. and Rymer, Jon Thomson and Ryan, Sean M. and Sammons, Megan and Scott, Anne K. and Scott, Ashley L. and Shinomiya, Aya and Smith, Claire and Smith, Kelsey and Smith, Natalie L. and Sobeski, Margaret A. and Suleiman, Alia and Swift, Jackie and Takemura, Satoko and Talebi, Iris and Tarnogorska, Dorota and Tenshaw, Emily and Tokhi, Temour and Walsh, John J. and Yang, Tansy and Horne, Jane Anne and Li, Feng and Parekh, Ruchi and Rivlin, Patricia K and Jayaraman, Vivek and Costa, Marta and Jefferis, Gregory SXE and Ito, Kei and Saalfeld, Stephan and George, Reed and Meinertzhagen, Ian and Rubin, Gerald M and Hess, Harald F and Jain, Viren and Plaza, Stephen M (2020) A connectome and analysis of the adult Drosophila central brain​eLife

  • Alexander S. Bates, James D. Manton, Sridhar R. Jagannathan, Marta Costa, Philipp Schlegel, Torsten Rohlfing, Gregory S. X. E. Jefferis (2020) The natverse, a versatile computational toolbox to combine and analyse neuroanatomical dataeLife

  • 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 and Scott Waddell (2018) Integration of Parallel Opposing Memories Underlies Memory ExtinctionCell
  • Robert Court, Shigehiro Namiki, J. Douglas Armstrong, Jana Börner, Gwyneth Card, Marta Costa, Michael Dickinson, Carsten Duch, Wyatt Korff, Richard Mann, David Merritt, Rod K. Murphey, Andrew M. Seeds, Troy Shirangi, Julie H. Simpson, James W. Truman, John C. Tuthill, Darren W. Williams and David Shepherd (2020) A Systematic Nomenclature for the Drosophila Ventral Nerve Cord. Neuron

  • Araya, C., Tawk, M., Girdler, G. C., Costa, M., Carmona-Fontaine, C. and Clarke, J. D. (2014).Mesoderm is required for coordinated cell movements within zebrafish neural plate in vivo. Neural Dev. 9, 9.

  • Correia, C. (1), Costa, M. (1), Moraes, F. (1), Bom J., Nóvoa A. and Mallo, M. (2007). Bmp2 is required for migration but not for induction of neural crest cells in the mouse. Developmental Dynamics 236, 2493-2501. (1) equal contributors.

Senior Research Associate

Contact Details

Room 306, Austin Building
Department of Zoology
Downing Street
Cambridge, CB2 3EJ UK
01223 (3)34455


Person keywords: 
Image Visualisation
Electon Microscopy
Cellular and Molecular Neuroscience
computational neuroanatomy
Imaging technologies