Toward automatic phenotyping of developing embryos from videos

Feng Ning, Damien Delhomme, Yann LeCun, Fabio Piano, Léon Bottou, Paolo Emilio Barbano

Research output: Contribution to journalArticlepeer-review


We describe a trainable system for analyzing videos of developing C. elegans embryos. The system automatically detects, segments, and locates cells and nuclei in microscopic images. The system was designed as the central component of a fully automated phenotyping system. The system contains three modules 1) a convolutional network trained to classify each pixel into five categories: cell wall, cytoplasm, nucleus membrane, nucleus, outside medium; 2) an energy-based model, which cleans up the output of the convolutional network by learning local consistency constraints that must be satisfied by label images; 3) a set of elastic models of the embryo at various stages of development that are matched to the label images.

Original languageEnglish (US)
Pages (from-to)1360-1371
Number of pages12
JournalIEEE Transactions on Image Processing
Issue number9
StatePublished - Sep 2005


  • Convolutional network
  • Energy-based model
  • Image segmentation
  • Nonlinear filter

ASJC Scopus subject areas

  • Software
  • Computer Graphics and Computer-Aided Design


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