Publications of the department "Electrons - Photons - Neurons"

Kornfeld, J.; Wang, Y.; Januszewski, M.; Rother, A.; Schubert, P.; Goldmann, M.; Jain, V.; Denk, W.; Fee, M. S.: An anatomical substrate of credit assignment in reinforcement learning. bioRxiv: the preprint server for biology (2026)

Rother, A.; Januszewski, M.; Jain, V.; Fee, M.S.; Kornfeld, J.: The songbird basal ganglia connectome. bioRxiv: the preprint server for biology (2026)

Rickgauer, J. P.; Choi, H.; Moore, A. S.; Denk, W.; Lippincott-Schwartz, J.: Structural dynamics of human ribosomes in situ reconstructed by exhaustive high-resolution template matching. Molecular Cell 84 (24), pp. 4912 - 4928 (2024)

Schubert, P. J.; Saxena, R.; Kornfeld, J.: DeepFocus: Fast focus and astigmatism correction for electron microscopy. Nature Communications 15, 948 (2024)

Kappel, J. M.; Förster, D.; Slangewal, K.; Shainer, I.; Svara, F. N.; Donovan, J.; Sherman, S.; Januszewski, M.; Baier, H.; Larsch, J.: Visual recognition of social signals by a tectothalamic neural circuit. Nature 608 (7921), pp. 146 - 152 (2022)

Schubert, P. J.; Dorkenwald, S.; Januszewski, M.; Klimesch, J.; Svara, F. N.; Mancu, A.; Ahmad, H.; Fee, M. S.; Jain, V.; Kornfeld, J.: SyConn2: Dense synaptic connectivity inference for volume electron microscopy. Nature Methods 19 (11), pp. 1367 - 1370 (2022)

Svara, F. N.; Förster, D.; Kubo, F.; Januszewski, M.; Dal Maschio, M.; Schubert, P. J.; Kornfeld, J.; Wanner, A. A.; Laurell, E.; Denk, W. et al.; Baier, H.: Automated synapse-level reconstruction of neural circuits in the larval zebrafish brain. Nature Methods 19 (11), pp. 1357 - 1366 (2022)

Abbott, L. F.; Bock, D. D.; Callaway, E. M.; Denk, W.; Dulac, C.; Fairhall, A. L.; Fiete, I.; Harris, K. M.; Helmstaedter, M.; Jain, V. et al.; Kasthuri, N.; LeCun, Y.; Lichtman, J. W.; Littlewood, P. B.; Luo, L.; Maunsell, J. H. R.; Reid, R. C.; Rosen, B. R.; Rubin, G. M.; Sejnowski, T. J.; Seung, H. S.; Svoboda, K.; Tank, D. W.; Tsao, D.; Van Essen, D. C.: The mind of a mouse. Cell 182 (6), pp. 1372 - 1376 (2020)

Egger, R.; Tupikov, Y.; Elmaleh, M.; Katlowitz, K. A.; Benezra, S. E.; Picardo, M. A.; Moll, F.; Kornfeld, J.; Jin, D. Z.; Long, M. A.: Local axonal conduction shapes the spatiotemporal properties of neural sequences. Cell 183 (2), pp. 537 - 548.e12 (2020)

Martins, J. C.; Saxena, R.; Neppl, S.; Alhazmi, A.; Reiner, M.; Veloza, S.; Belka, C.; Parodi, K.: Optimization of phase space files from clinical linear accelerators. Physica Medica 64, pp. 54 - 68 (2019)

Schubert, P. J.; Dorkenwald, S.; Januszewski, M.; Jain, V.; Kornfeld, J.: Learning cellular morphology with neural networks. Nature Communications 10, 2736 (2019)

Boergens, K. M.; Kapfer, C.; Helmstaedter, M.; Denk, W.; Borst, A.: Full reconstruction of large lobula plate tangential cells in Drosophila from a 3D EM dataset. PLoS One 13 (11), e0207828 (2018)

Januszewski, M.; Kornfeld, J.; Li, P. H.; Pope, A.; Blakely, T.; Lindsey, L.; Maitin-Shepard, J.; Tyka, M.; Denk, W.; Jain, V.: High-precision automated reconstruction of neurons with flood-filling networks. Nature Methods 15 (8), pp. 605 - 610 (2018)

Kornfeld, J.; Denk, W.: Progress and remaining challenges in high-throughput volume electron microscopy. Current Opinion in Neurobiology 50, pp. 261 - 267 (2018)

Kubota, Y.; Sohn, J.; Hatada, S.; Schurr, M.; Straehle, J.; Gour, A.; Neujahr, R.; Miki, T.; Mikula, S.; Kawaguchi, Y.: A carbon nanotube tape for serial-section electron microscopy of brain ultrastructure. Nature Communications 9, 437 (2018)

Svara, F. N.; Kornfeld, J.; Denk, W.; Bollmann, J. H.: Volume EM reconstruction of spinal cord reveals wiring specificity in speed-related motor circuits. Cell Reports 23 (10), pp. 2942 - 2954 (2018)

Dorkenwald, S.; Schubert, P. J.; Killinger, M. F.; Urban, G.; Mikula, S.; Svara, F. N.; Kornfeld, J.: Automated synaptic connectivity inference for volume electron microscopy. Nature Methods 14 (4), pp. 435 - 442 (2017)

Kornfeld, J.; Benezra, S. E.; Narayanan, R. T.; Svara, F. N.; Egger, R.; Oberlaender, M.; Denk, W.; Long, M. A.: EM connectomics reveals axonal target variation in a sequence-generating network. eLife 6, e24364 (2017)

Rickgauer, J. P.; Grigorieff, N.; Denk, W.: Single-protein detection in crowded molecular environments in cryo-EM images. eLife 6, e25648 (2017)

Mikula, S.: Progress towards mammalian whole-brain cellular connectomics. Frontiers in Neuroanatomy 10, 62 (2016)

Mikula, S.; Denk, W.: High-resolution whole-brain staining for electron microscopic circuit reconstruction. Nature Methods 12 (6), pp. 541 - 546 (2015)