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2 Janelia Publications

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    09/26/18 | Synaptic cleft segmentation in non-isotropic volume electron microscopy of the complete Drosophila brain.
    Heinrich L, Funke J, Pape C, Nunez-Iglesias J, Saalfeld S
    Medical Image Computing and Computer Assisted Intervention – MICCAI 2018. 2018 Sep 26:317-25. doi: 10.1007/978-3-030-00934-2_36

    Neural circuit reconstruction at single synapse resolution is increasingly recognized as crucially important to decipher the function of biological nervous systems. Volume electron microscopy in serial transmission or scanning mode has been demonstrated to provide the necessary resolution to segment or trace all neurites and to annotate all synaptic connections. 
    Automatic annotation of synaptic connections has been done successfully in near isotropic electron microscopy of vertebrate model organisms. Results on non-isotropic data in insect models, however, are not yet on par with human annotation. 
    We designed a new 3D-U-Net architecture to optimally represent isotropic fields of view in non-isotropic data. We used regression on a signed distance transform of manually annotated synaptic clefts of the CREMI challenge dataset to train this model and observed significant improvement over the state of the art. 
    We developed open source software for optimized parallel prediction on very large volumetric datasets and applied our model to predict synaptic clefts in a 50 tera-voxels dataset of the complete Drosophila brain. Our model generalizes well to areas far away from where training data was available.

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    05/24/18 | The candidate multi-cut for cell segmentation.
    Funke J, Zhang C, Pietzsch T, Gonzalez Ballester MA, Saalfeld S
    2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018). 2017 Jul 04:. doi: 10.1109/ISBI.2018.8363658

    Two successful approaches for the segmentation of biomedical images are (1) the selection of segment candidates from a merge-tree, and (2) the clustering of small superpixels by solving a Multi-Cut problem. In this paper, we introduce a model that unifies both approaches. Our model, the Candidate Multi-Cut (CMC), allows joint selection and clustering of segment candidates from a merge-tree. This way, we overcome the respective limitations of the individual methods: (1) the space of possible segmentations is not constrained to candidates of a merge-tree, and (2) the decision for clustering can be made on candidates larger than superpixels, using features over larger contexts. We solve the optimization problem of selecting and clustering of candidates using an integer linear program. On datasets of 2D light microscopy of cell populations and 3D electron microscopy of neurons, we show that our method generalizes well and generates more accurate segmentations than merge-tree or Multi-Cut methods alone.

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