Lab members
- Elizabeth Barsotti, publications
- Albert Cardona (personal page, external personal page), github, publications
- Jiaqi Chen
- Marc Corrales, github, publications
- Ana Correia, publications
- Daniel Franco Barranco, github, publications
- Pedro Gómez Gálvez, publications
- Shi Yan Lee
- Laura Lungu, publications
- Samia Mohinta, github, publications
- Scott Wilson
- Yudi Wu
- Yijie Yin, publications
See former lab alumni.
Current lab preprints
- Ferreira Castro and Cardona, 2025. "Invariant synaptic density links neuronal activity stability and wiring optimisation principles across species" bioRxiv 2024.07.18.604056
- Yin, Y., et al. 2025. "The Connectome Interpreter Toolkit." bioRxiv 2025.09.29.679410
- Mohinta, S., Franco-Barranco, D., et al. 2025. "Towards generalized synapse detection across invertebrate species." arXiv:2509.17041
- Randel et al. 2025. "Combining brainwide activity imaging and electron microscopy reveals novel nociceptive circuits." bioRxiv 2025.09.25.678485
- Lungu et al. 2025. "The central complex of the larval fruit fly brain." bioRxiv 2025.09.30.679510
- Lee et al. 2025. "Beyond agreement: standardizing crowdsourced synapse annotations through proofreading in EM connectomics." 2025.09.26.678851
- Correia et al. 2025. "Mapping the nervous system of the Idiosepius hallami pygmy squid: insights from whole-animal X-ray nanotomography imaging." bioRxiv 2025.09.25.678516
- Eschbach et al. 2025. "A multisensory, bidirectional, valence encoder guides behavioral decisions." bioRxiv2025.09.26.678749
Selected publications
- Winding, M., Pedigo, B., et al. 2023."The connectome of an insect brain." Science 379.6636: eadd9330.
- Corrales, M., Cocanougher, B., et al. 2023. "A single-cell transcriptomic atlas of complete insect nervous systems across multiple life stages". Neural Development 17(1):8.
- Barnes et al. 2022. "Synaptic counts approximate synaptic contact area in Drosophila" PLoS ONE 17(4):e0266064, (bioRxiv 2020)
- Eschbach C., Fushiki A. et al. 2021. "Circuits for integrating learnt and innate valences in the fly brain". eLife 62567 (bioRxiv 2020)
- Eschbach C., Fushiki A. et al. 2020. "Recurrent architecture for adaptive regulation of learning in the insect brain". Nature Neuroscience 23(4):544-555 (bioRxiv 2019)
- Valdes-Aleman, J. et al. 2020. "Comparative connectomics reveals how partner identity, location, and activity specify synaptic connectivity in Drosophila". Neuron 109(1):105-122.e7 (bioRxiv 2019)
- Eichler K., Li F., Litwin-Kumar A. et al. 2017. "The complete connectome of a learning and memory centre in an insect brain", Nature 548(7666):175-82 (bioRxiv 2017)
- Gerhard S. et al. 2017. "Conserved neural circuit structure across Drosophila larval development revealed by comparative connectomics". eLife 6:e29089 (bioRxiv 2017)
- Schneider-Mizell CM., Gerhard S. et al. 2016. "Quantitative neuroanatomy for connectomics in Drosophila". eLife 5: e12059
- Jovanic T., Schneider-Mizell, CM. et al. 2016 "Competitive disinhibition mediates behavioral choice and sequences in Drosophila". Cell 167(3):858-870
- Zwart M. et al. 2016. "Selective inhibition mediates the sequential recruitment of motor pools". Neuron 91(3):615-628
- Fushiki A. et al. 2016. "A circuit mechanism for the propagation of waves of muscle contraction in Drosophila". eLife 5:e13253
- Berck ME, Khandelwal A. et al. 2016. "The wiring diagram of a glomerular olfactory system". eLife 5:e14859
- Ohyama T., Schneider-Mizell CM et al. 2015. "A multilevel multimodal circuit enhances action selection in Drosophila". Nature 520(7549):633-639
Selected prior publications
- Schindelin, J. et al. 2012. "Fiji: an open-source platform for biological-image analysis". Nature Methods 9(7):676--682.
- Cardona, A. et al. 2012. "TrakEM2 Software for Neural Circuit Reconstruction". PLoS ONE 7(6):e38011.
- Saalfeld, S. et al. 2012. "Elastic volume reconstruction from series of ultra-thin microscopy sections". Nature Methods 9(70):717--720.
Resources
- Published neurons and circuits of the Drosophila central nervous system in the first instar larva, as reconstructed from serial section electron microscopy. Accessible with the open source CATMAID software (github repository and documentation). Kindly hosted by the Virtual Fly Brain.
- CATMAID open source software for connectomics (github; documentation).
- Fiji python tutorial: learn image processing with the open source software Fiji (is Just ImageJ) and the python programming language.
- TrakEM2 software and user manual. See also scripting tutorials in jython for TrakEM2 and the TrakEM2 wiki page with performance tips for the java virtual machine (JVM).
- ISBI 2012 image segmentation challenge data (30 serial sections, 512x512 pixels, of neural tissue with cytoplasmic membranes, synapses and mitochondria manually annotated by Albert Cardona.
- Chris L. Barnes, PhD student (2015--2019) and software engineer (2020--2024) github; publications
- Margjele Shala, master student (2022--2023).
- André Castro, postdoc (2020--2023), publications
- Daniel Han, postdoc (2021--2023), publications
- Ayesha Khan, summer student (August and September, 2021).
- Xinyu Tang, visiting undergraduate student (October 2019 to March 2020).
- Rebecca Arruda, technician (2018--2019)
- Matthew E. Berck, postdoc (2017--2018), publications
- Akira Fushiki, visiting student (2013, 2014) and postdoc (2015--2017), publications
- Elise Croteau-Chonka, undergraduate summer student (2013) and technician (2016), publications
- Andrew Champion, software engineer (2014--2016) and graduate student (2016--2020), github, publications
- Li Feng, postdoc (2014--2017), publications
- Maarten Zwart, postdoc (2013--2016), publications
- Mei Shao, senior electrophysiologist (2013--2019)
- Tom Kazimiers, software engineer (2013--2019), github, publications
- Brittany Kemp, technician (Summer 2013)
- Laura Herren, technician (2013)
- Waleed Osman, technician (2013)
- Ingrid Andrade, visiting student (2012) and technician (2013--2015), publications
- Jan Funke, graduate student, co-supervised with Matthew Cook (2010--2014), github, publications
- Stephan Gerhard, graduate student (2011--2015), github, publications
- Alex Berthold van der Bourg, master student (2011-2012), publications
- Kenny Floria, undergraduate researcher (2010)
- Casey Schneider-Mizell, postdoc (2010--2017), github, publications
- Mark Longair, postdoc and software engineer (2009--2012), github, publications
- Ignacio Arganda Carreras, postdoc (2009--2010), github, publications
- Stephan Saalfeld, master student (2008), co-supervised together with Pavel Tomancak, github, lab's github, publications