Biblio

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2026
Lian Y, Adjavon D-Y, Kawase T, Kim J, Fleishman G, Preibisch S, Funke J, Liu ZJ.  2026.  Machine learning-guided spatial omics for tissue-scale discovery of cell-type-specific architectures. bioRxiv.
Gillet V, Sayre ME, Badalamente GS, Schieber NL, Tedore K, Funke J, Heinze S.  2026.  A multi-resolution imaging and analysis pipeline for comparative circuit reconstruction in insects. bioRxiv.
Gillet V, Sayre ME, Badalamente GS, Schieber NL, Tedore K, Funke J, Heinze S.  2026.  A multi-resolution imaging and analysis pipeline for comparative circuit reconstruction in insects. eLife.
2025
Hillsley A, Stein J, Tillberg PW, Stern DL, Funke J.  2025.  A Bayesian model to count the number of two-state emitters in a diffraction limited spot.. Nano Lett.
Park SYun, Sheridan A, An B, Jarvis E, Lyudchik J, Patton W, Axup JY, Chan SW, Damstra HGJ, Leible D et al..  2025.  Combinatorial protein barcodes enable self-correcting neuron tracing with nanoscale molecular context. bioRxiv.
Bates AShakeel, Phelps JS, Kim M, Yang HH, Matsliah A, Ajabi Z, Perlman E, Delgado KM, Osman MAbdal Moni, Salmon CK et al..  2025.  Distributed control circuits across a brain-and-cord connectome. bioRxiv.
Lalit M, Funke J.  2025.  An investigation of unsupervised cell tracking and interactive fine-tuning. 2025 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW).
Berg S, Beckett IR, Costa M, Schlegel P, Januszewski M, Marin EC, Nern A, Preibisch S, Qiu W, Takemura S-ya et al..  2025.  Sexual dimorphism in the complete connectome of the Drosophila male central nervous system. bioRxiv.
Funke J.  2025.  Uncertainty quantification for connectomics.. Nat Methods. 22(12):2484-2486.
2024
Patton W, Rhoades JL, Zouinkhi M, Ackerman DG, Malin-Mayor C, Adjavon D, Heinrich L, Bennett D, Zubov Y, Team CMProject et al..  2024.  DaCapo: a modular deep learning framework for scalable 3D image segmentation. arXiv.
Shiu PK, Sterne GR, Spiller N, Franconville R, Sandoval A, Zhou J, Simha N, Kang CHyuk, Yu S, Kim JS et al..  2024.  A Drosophila computational brain model reveals sensorimotor processing.. Nature. 634(8032):210-219.
Dorkenwald S, Matsliah A, Sterling AR, Schlegel P, Yu S-C, McKellar CE, Lin A, Costa M, Eichler K, Yin Y et al..  2024.  Neuronal wiring diagram of an adult brain.. Nature. 634(8032):124-138.
Eckstein N, Bates AShakeel, Champion A, Du M, Yin Y, Schlegel P, Lu AKun-Yang, Rymer T, Finley-May S, Paterson T et al..  2024.  Neurotransmitter classification from electron microscopy images at synaptic sites in Drosophila melanogaster. Cell. 187(10):2574-2594.e23.
Adjavon D-Y, Eckstein N, Bates AS, Jefferis GSXE, Funke J.  2024.  Quantitative Attributions with Counterfactuals. bioRxiv.
Hillsley A, Adhikari R, Johnson ADowdell, Espinosa-Medina I, Funke J, Feliciano D.  2024.  Spatial single-cell Organellomics reveals nutrient dependent hepatocyte heterogeneity and predicts pathophysiological status in vivo. bioRxiv.
2023
Malin-Mayor C, Hirsch P, Guignard L, McDole K, Wan Y, Lemon WC, Kainmueller D, Keller PJ, Preibisch S, Funke J.  2023.  Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations.. Nature Biotechnology. 41(1):44-49.
Sheridan A, Nguyen TM, Deb D, Lee W-CAllen, Saalfeld S, Turaga SC, Manor U, Funke J.  2023.  Local shape descriptors for neuron segmentation.. Nature Methods. 20(2):295-303.
Nguyen TM, Thomas LA, Rhoades JL, Ricchi I, Yuan XCindy, Sheridan A, Hildebrand DGC, Funke J, Regehr WG, Lee W-CAllen.  2023.  Structured cerebellar connectivity supports resilient pattern separation.. Nature. 613(7944):543-549.
Heinrich L, Patton W, Bennett D, Ackerman D, Park G, Bogovic JA, Eckstein N, Petruncio A, Clements J, Pang S et al..  2023.  Towards Generalizable Organelle Segmentation in Volume Electron Microscopy.. Microscopy and Microanalysis. 29(Supplement_1):975.
Wolf S, Lalit M, McDole K, Funke J.  2023.  Unsupervised Learning of Object-Centric Embeddings for Cell Instance Segmentation in Microscopy Images. 2023 IEEE/CVF International Conference on Computer Vision (ICCV).
2022
Malin-Mayor C, Hirsch P, Guignard L, McDole K, Wan Y, Lemon WC, Kainmueller D, Keller PJ, Preibisch S, Funke J.  2022.  Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations.. Nature Biotechnology.
Baker CA, McKellar C, Pang R, Nern A, Dorkenwald S, Pacheco DA, Eckstein N, Funke J, Dickson BJ, Murthy M.  2022.  Neural network organization for courtship-song feature detection in Drosophila.. Current Biology. 32(15):3317-3333.e7.
Zhu P-P, Hung H-F, Batchenkova N, Nixon-Abell J, Henderson J, Zheng P, Renvoisé B, Pang S, C Xu S, Saalfeld S et al..  2022.  Transverse endoplasmic reticulum expansion in hereditary spastic paraplegia corticospinal axons.. Human Molecular Genetics.
Zhu P-P, Hung H-F, Batchenkova N, Nixon-Abell J, Henderson J, Zheng P, Renvoisé B, Pang S, C Xu S, Saalfeld S et al..  2022.  Transverse endoplasmic reticulum expansion in hereditary spastic paraplegia corticospinal axons.. Human Molecular Genetics. 31(16):2779-2795.
2021
Buhmann J, Sheridan A, Gerhard S, Krause R, Nguyen T, Heinrich L, Schlegel P, Lee W-CAllen, Wilson R, Saalfeld S et al..  2021.  Automatic Detection of Synaptic Partners in a Whole-Brain Drosophila EM Dataset. Nature Methods. 18(7):771-4.