SPEX2

The software tool SPEX2 is an automatic system for embryonic in situ hybridization (ISH) image processing, which extracts, transforms, compares, classifies, and clusters spatial gene expression patterns in Drosophila embryos. The pipeline for gene expression pattern extraction outputs the precise spatial locations and strengths of gene expression. SPEX2 achieves excellent performance in automatic image annotation, and also finds clusters that are significantly enriched for gene ontology functional annotations and annotation terms from a controlled vocabulary used by human curators to describe these images.

Topic

Gene expression;Genetics;RNA;Ontology and terminology

Detail

  • Operation: Image analysis;Gene expression analysis

  • Software interface: Command-line user interface

  • Language: MATLAB

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: National Science Foundation DBI, Alfred P. Sloan Fellowship.

  • Input: -

  • Output: -

  • Contact: epxing@cs.cmu.edu;mdeptola@cs.cmu.edu

  • Collection: -

  • Maturity: -

Publications

  • SPEX2: automated concise extraction of spatial gene expression patterns from Fly embryo ISH images.
  • Puniyani K, et al. SPEX2: automated concise extraction of spatial gene expression patterns from Fly embryo ISH images. SPEX2: automated concise extraction of spatial gene expression patterns from Fly embryo ISH images. 2010; 26:i47-56. doi: 10.1093/bioinformatics/btq172
  • https://doi.org/10.1093/bioinformatics/btq172
  • PMID: 20529936
  • PMC: PMC2881357

Download and documentation

    Currently not available or not maintained.

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