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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.
Sheridan A, Nguyen T, Deb D, Lee W-CAllen, Saalfeld S, Turaga S, Manor U, Funke J.  2021.  Local Shape Descriptors for Neuron Segmentation. bioRxiv.
Maniates-Selvin JT, Hildebrand DGrant Colb, Graham BJ, Kuan AT, Thomas LA, Nguyen T, Buhmann J, Azevedo AW, Shanny BL, Funke J et al..  2021.  Reconstruction of motor control circuits in adult Drosophila using automated transmission electron microscopy. Cell. 184(3)
Lundberg E, Funke J, Uhlmann V, Gerlich D, Walter T, Carpenter A, Coehlo LPedro.  2021.  Which image-based phenotypes are most promising for using AI to understand cellular functions and why? Cell Systems. 12(5):384-387.
Heinrich L, Bennett D, Ackerman D, Park W, Bogovic J, Eckstein N, Petruncio A, Clements J, Pang S, C Xu S et al..  2021.  Whole-cell organelle segmentation in volume electron microscopy.. Nature. 599(7883):141-46.
2020
Kuan AT, Phelps JS, Thomas LA, Nguyen TM, Han J, Chen C-L, Azevedo AW, Tuthill JC, Funke J, Cloetens P et al..  2020.  Dense neuronal reconstruction through X-ray holographic nano-tomography.. Nature Neuroscience. 23(12):1637-43.
Wolf S, Hamprecht FA, Funke J.  2020.  Inpainting Networks Learn to Separate Cells in Microscopy Images. British Machine Vision Conference.
2019
Funke J, Tschopp FD, Grisaitis W, Sheridan A, Singh C, Saalfeld S, Turaga SC.  2019.  Large scale image segmentation with structured loss based deep learning for connectome reconstruction.. IEEE Transactions on Pattern Analysis and Machine Intelligence. 41(7):1669-80.
2018
Plaza SM, Funke J.  2018.  Analyzing image segmentation for connectomics.. Frontiers in Neural Circuits. 12:102.
Heinrich L, Funke J, Pape C, Nunez-Iglesias J, Saalfeld S.  2018.  Synaptic cleft segmentation in non-isotropic volume electron microscopy of the complete Drosophila brain.. Medical Image Computing and Computer Assisted Intervention – MICCAI 2018. :317-25.