Feature Augmented Deep Neural Networks for Segmentation of Cells

  • Sajith Kecheril SadanandanEmail author
  • Petter Ranefall
  • Carolina Wählby
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9913)


In this work, we use a fully convolutional neural network for microscopy cell image segmentation. Rather than designing the network from scratch, we modify an existing network to suit our dataset. We show that improved cell segmentation can be obtained by augmenting the raw images with specialized feature maps such as eigen value of Hessian and wavelet filtered images, for training our network. We also show modality transfer learning, by training a network on phase contrast images and testing on fluorescent images. Finally we show that our network is able to segment irregularly shaped cells. We evaluate the performance of our methods on three datasets consisting of phase contrast, fluorescent and bright-field images.


Deep neural network Feature augmentation Cell segmentation Convolutional neural network Unstained cells 



This work was supported by the Swedish research council under Grant 2012-4968 (to CW) and the Swedish strategic research program eSSENCE. Image data was kindly provided by Johan Elf at the Department of Cell and Molecular Biology, Computational and Systems Biology, Uppsala University, Sweden and Theresa Vincent at the Department of Physiology and Pharmacology, Karolinska Institutet, Sweden.


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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Sajith Kecheril Sadanandan
    • 1
    • 2
    Email author
  • Petter Ranefall
    • 1
    • 2
  • Carolina Wählby
    • 1
    • 2
  1. 1.Department of Information TechnologyUppsala UniversityUppsalaSweden
  2. 2.SciLifeLabUppsalaSweden

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