Development Genes and Evolution

, Volume 215, Issue 7, pp 374–381 | Cite as

A high-throughput method for quantifying gene expression data from early Drosophila embryos

  • Hilde Janssens
  • Dave Kosman
  • Carlos E. Vanario-Alonso
  • Johannes Jaeger
  • Maria Samsonova
  • John Reinitz
Technical Note


We describe an automated high-throughput method to measure protein levels in single nuclei in blastoderm embryos of Drosophila melanogaster by means of immunofluorescence. The method consists of a chain of specific algorithms assembled into an image processing pipeline. This pipeline transforms a confocal scan of an embryo stained with fluorescently tagged antibodies into a text file. This text file contains a numerical identifier for each nucleus, the coordinates of its centroid, and the average concentrations of three proteins in that nucleus. The central algorithmic component of the method is the automatic identification of nuclei by edge detection with the use of watersheds as an error-correction step. This method provides high-throughput quantification at cellular resolution.


Image segmentation Mathematical morphology Insect segmentation Drosophila blastoderm 

Supplementary material

427_2005_484_ESM_supp.pdf (949 kb)
(949 KB)


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Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • Hilde Janssens
    • 1
  • Dave Kosman
    • 2
  • Carlos E. Vanario-Alonso
    • 1
    • 3
  • Johannes Jaeger
    • 1
  • Maria Samsonova
    • 4
  • John Reinitz
    • 1
  1. 1.Department of Applied Mathematics and Statistics, and Center for Developmental GeneticsStony Brook UniversityStony BrookUSA
  2. 2.Department of BiologyUniversity of CaliforniaSan DiegoUSA
  3. 3.Universidade Federal do Rio de JaneiroInstituto de Biofísica Carlos Chagas FilhoRio de JaneiroBrazil
  4. 4.Department of Computational Biology, Center of Advanced StudiesSt. Petersburg State Polytechnic UniversitySt. PetersburgRussia

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