title: A high-throughput method for quantifying gene expression data from early Drosophila embryos.
abstract: 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.
authors.affiliation: Department of Applied Mathematics and Statistics, and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY 11794-3600, USA.
authors.forename: Hilde
authors.initials: H
authors.lastname: Janssens
authors.forename: Dave
authors.initials: D
authors.lastname: Kosman
authors.forename: Carlos E
authors.initials: CE
authors.lastname: Vanario-Alonso
authors.forename: Johannes
authors.initials: J
authors.lastname: Jaeger
authors.forename: Maria
authors.initials: M
authors.lastname: Samsonova
authors.forename: John
authors.initials: J
authors.lastname: Reinitz
mesh_terms: D000465:Algorithms; D000818:Animals; D018951:Antigens, CD20 / Q000378:metabolism; D004330:Drosophila / Q000196:embryology* / Q000235:genetics*; D029721:Drosophila Proteins / Q000235:genetics / Q000378:metabolism; D004625:Embryo, Nonmammalian / Q000378:metabolism; D019085:Fluorescent Antibody Technique, Direct; D018507:Gene Expression Regulation, Developmental; D017344:Genes, Insect; D006454:Hemoglobins / Q000378:metabolism; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism; D007091:Image Processing, Computer-Assisted; D019476:Insect Proteins / Q000235:genetics / Q000378:metabolism; D018613:Microscopy, Confocal; D013997:Time Factors; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D018951:Antigens, CD20; D029721:Drosophila Proteins; D006454:Hemoglobins; D018398:Homeodomain Proteins; D019476:Insect Proteins; D014157:Transcription Factors; C052837:eve protein, Drosophila