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Murphy Lab - Software - Nature Methods OMERO.searcher

The software and data used for the following paper can be downloaded below:

B.H. Cho, I. Cao-Berg, J.A. Bakal, and R.F. Murphy (2012) OMERO.searcher: Content-based image search for microscope images. Nature Methods 9:633-634.

The data and code are contained in .tgz files:

Source Code 63 Kb
Intermediate Results 65 Mb
ASCB Cell Library images (.tif format)
RandTag images (.bmp format)
874 Mb
32 Gb

Download & Expand Source Code, Intermediate Results and/or Data

All tarfiles are designed to untar into the appropriate directories within the directory Nature_Methods_OMERO.searcher. Please make sure to run the following commands from the same top level directory. Be aware that the RandTag images tarfiles will expand to approximately 140G total.
>> tar -xzvf Nature_Methods_OMERO.searcher.tgz
>> tar -xzvf Nature_Methods_OMERO.searcher_intermediate.tgz
>> tar -xzvf Nature_Methods_OMERO.searcher_RandTag_original.tgz
>> tar -xzvf Nature_Methods_OMERO.searcher_ASCB.tgz

Recreating Results from Raw Image Data

  • To recreate the results from the article from raw image data, download the source and data from the above links and untar according to instructions above.

  • >> cd Nature_Methods_OMERO.searcher
    >> sh generate_intermediate_from_images.sh
    >> sh generate_figures_from_intermediate.sh

Recreating Results from Intermediate Results

  • To recreate the results from the article from intermediate results, i.e. the 6 figures, download the source code and intermediate results from the above links and untar according to instructions above.
  • Make sure the directory Nature_Methods_OMERO.searcher/intermediate_results exists
    >> cd Nature_Methods_OMERO.searcher
    >> sh generate_figures_from_intermediate.sh
This code has been tested on Python 2.7 for Linux x86_64.

System requirements

  • Python 2.7 + following python packages
    • numpy
    • scipy
    • mahotas

Last Updated: 07 Oct 2013

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