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Journal Article
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.
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.
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.
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.
Funke J, Klein J, Moreno-Noguer F, Cardona A, Cook M.  2017.  TED: A Tolerant Edit Distance for segmentation evaluation.. Methods. 115:119-27.
Buhmann J, Krause R, Lentini RCeballos, Eckstein N, Cook M, Turaga SC, Funke J.  2018.  Synaptic partner prediction from point annotations in insect brains.. MICCAI 2018: Medical Image Computing and Computer Assisted Intervention.
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.
Funke J, Klein J, Moreno-Noguer F, Cardona A, Cook M.  2016.  Structured learning of assignment models for neuron reconstruction to minimize topological errors.. IEEE 13th International Symposium on Biomedical Imaging (ISBI). :607-11.
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.
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)
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.
Dorkenwald S, Matsliah A, Sterling AR, Schlegel P, Yu S-C, McKellar CE, Lin A, Costa M, Eichler K, Yin Y et al..  2023.  Neuronal wiring diagram of an adult brain.. bioRxiv.
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.
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.
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.
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.
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.
Funke J, Zhang C, Pietzsch T, Ballester MAGonzalez, Saalfeld S.  2017.  The candidate multi-cut for cell segmentation.. 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018).
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.
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.
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.
Plaza SM, Funke J.  2018.  Analyzing image segmentation for connectomics.. Frontiers in Neural Circuits. 12:102.
Conference Paper
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).
Wolf S, Hamprecht FA, Funke J.  2020.  Inpainting Networks Learn to Separate Cells in Microscopy Images. British Machine Vision Conference.