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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