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Open Access Technical Note

Spatial gene expression quantification: a tool for analysis of in situ hybridizations in sea anemone Nematostella vectensis

Daniel Botman and Jaap A Kaandorp*

Author Affiliations

Section Computational Science, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands

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BMC Research Notes 2012, 5:555  doi:10.1186/1756-0500-5-555

Published: 5 October 2012

Additional files

Additional file 1:

Matlab programs: “genexp.m” for cell layer decomposition of gene expression images and profile editing; “oneview.m” for a 2D gene expression array from a single decomposed image; “twoviews.m” for a 2D array from a decomposed image and perpendicular view. Supporting files: Matlab user interface “genexp.fig” (necessary to run “genexp.m”); directory “embryodata” containing geometry definitions; directory “functions” containing Matlab functions used in the main programs. Matlab script: “stanpro.m” for creating a standardized 1D array from a GENEXP profile figure. Manuals: “readme_genexp.m” for GENEXP program; “readme_oneview.m” for ONEVIEW program; “readme_twoviews.m” for TWOVIEWS program.

Format: TAR Size: 290KB Download file

Open Data