Computational Regulatory Genomics

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Imaging pipeline

A microfluidic device for automated high throughput live imaging of gene expression

W. Busch,  B. Moore,  B. Martsberger,  D. Mace,  R. Twigg,  J. Jung,  I. Pruteanu-Malinici,  S. Kennedy,  G. Fricke,  R. Clark,  U. Ohler,  P. Benfey (2012). A microfluidic device and computational platform for high-throughput live imaging of gene expression. Nature Methods.


Imaging pipeline


We have developed an imaging pipeline that includes automated tracking of growing roots, automated image acquisition and gene expression quantification. Software may be downloaded (compressed) here.

The download contains the following applications:

  • RootAnalyze
    • A series of Matlab scripts for the offline quantification of gene expression from confocal fluorescence images.
  • RootArrayController
    • A Java application for the online automated acquisition of confocal fluorescence images. Currently implemented to work with a Zeiss LSM510.
  • RootSegmentation
    • A Java/C++ application for the segmentation of images (trained for low resolution images of plant roots).
  • RootSegmentationEvaluatio
    • A Java application (also requires Fiji) used to evaluate the performance of variance segmentation algorithms against a manually-labeled gold standard.
  • Stitcher Wrapper
    • A command-line wrapper around the Fiji Stitching plugin
  • ZoneMarker
    • A Fiji plugin (written in Java) for the manual annotation of longitudinal zones and quality control of the medial sections of high resolution images.
    This material is based upon work supported by the National Science Foundation under Grant No 0953184 (DBI CAREER award -- Advances in biological informatics).


    The RootArray Controller software can be assessed via:

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