Publication

Large scale image segmentation with structured loss based deep learning for connectome reconstruction

Journal Article (2019)

Journal

IEEE Transactions on Pattern Analysis and Machine Intelligence

Pages

1669-1680

Volume

41

Number

7

Doc link

http://dx.doi.org/10.1109/TPAMI.2018.2835450

File

Download the digital copy of the doc pdf document

Authors

  • Funke, Jan

  • Tschopp, Fabian

  • Grisaitis, William

  • Sheridan, Arlo

  • Singh, Chandan

  • Saalfeld, Stephan

  • Turaga, Srinivas C.

Abstract

We present a method combining affinity prediction with region agglomeration, which improves significantly upon the state of the art of neuron segmentation from electron microscopy (EM) in accuracy and scalability. Our method consists of a 3D U-net, trained to predict affinities between voxels, followed by iterative region agglomeration. We train using a structured loss based on MALIS, encouraging topologically correct segmentations obtained from affinity thresholding. Our extension consists of two parts: First, we present a quasi-linear method to compute the loss gradient, improving over the original quadratic algorithm. Second, we compute the gradient in two separate passes to avoid spurious gradient contributions in early training stages. Our predictions are accurate enough that simple learning-free percentile-based agglomeration outperforms more involved methods used earlier on inferior predictions. We present results on three diverse EM datasets, achieving relative improvements over previous results of 27%, 15%, and 250%. Our findings suggest that a single method can be applied to both nearly isotropic block-face EM data and anisotropic serial sectioned EM data. The runtime of our method scales linearly with the size of the volume and achieves a throughput of ~2.6 seconds per megavoxel, qualifying our method for the processing of very large datasets.

Categories

image recognition.

Scientific reference

J. Funke, F. Tschopp, W. Grisaitis, A. Sheridan, C. Singh, S. Saalfeld and S.C. Turaga. Large scale image segmentation with structured loss based deep learning for connectome reconstruction. IEEE Transactions on Pattern Analysis and Machine Intelligence, 41(7): 1669-1680, 2019.