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Combining Deep Learning and Active Contours Opens The Way to Robust, Automated Analysis of Brain Cytoarchitectonics

Part of the Lecture Notes in Computer Science book series (LNIP,volume 11046)


Deep learning has thoroughly changed the field of image analysis yielding impressive results whenever enough annotated data can be gathered. While partial annotation can be very fast, manual segmentation of 3D biological structures is tedious and error-prone. Additionally, high-level shape concepts such as topology or boundary smoothness are hard if not impossible to encode in Feedforward Neural Networks. Here we present a modular strategy for the accurate segmentation of neural cell bodies from light-sheet microscopy combining mixed-scale convolutional neural networks and topology-preserving geometric deformable models. We show that the network can be trained efficiently from simple cell centroid annotations, and that the final segmentation provides accurate cell detection and smooth segmentations that do not introduce further cell splitting or merging.


  • Histology
  • Image segmentation
  • Cell detection
  • Deep learning
  • Convolutional neural networks
  • Active contours

The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no. 616905.

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  • DOI: 10.1007/978-3-030-00919-9_21
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  1. 1.

    Related ideas integrating deep learning and level set formulations have been proposed by [14] or [6]. In contrast to our approach based on sparse centroid annotations these methods require pixel-accurate object masks for training.

  2. 2.

    Note that fastER is limited to 2D images only.

  3. 3.

    This would also speed up the entire pipeline as MGDM segmentation is the computationally more expensive part taking about 5 min for a \(256^3\) volume, while prediction with the MS-D net is about 10 times faster.


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Thierbach, K. et al. (2018). Combining Deep Learning and Active Contours Opens The Way to Robust, Automated Analysis of Brain Cytoarchitectonics. In: Shi, Y., Suk, HI., Liu, M. (eds) Machine Learning in Medical Imaging. MLMI 2018. Lecture Notes in Computer Science(), vol 11046. Springer, Cham.

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