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Murphy Lab - Software - OMERO.searcher


New Local Client features!
  • (1.3) Able to search multiple databases with the same feature set simultaneously
  • (1.3) Can match query image(s) to images at different resolutions
  • (1.2) Can search against your own content database using your own feature calculation code
New Content Databases available!
  • The Cell Library
  • Human Protein Atlas
There are three ways in which you can use OMERO.searcher.
You can use the OMERO.searcher External Search page of one or more OMERO databases that allow external searches, using images from your local computer (the local images do not have to be in any OMERO database or in any special format). The database that you search within must have OMERO.searcher installed and have enabled an External Search page (see item 3b below). The only requirement is that you have a compatible web browser (all major browsers are compatible) on your local computer.

The first public, externally searchable database that has been created is for demonstration and testing purposes associated with a Nature Methods manuscript describing OMERO.searcher. The database contains a subset of images from the RandTag project (Garcia Osuna et al, 2007).

The search page is http://omepslid2.compbio.cs.cmu.edu/content_search

You can run the OMERO.searcher Local Client on your local computer to search through any OMERO database for which you have access privileges (including the public externally searchable databases described above). This requires that your local computer have python and various python packages installed (see installation instructions for the Local Client). Due to issues with python configuration, this approach is far easier to use on Linux or Unix computers than on Mac OS or Windows computers. Download OMERO.searcher Local Client v1.3 View the Getting Started document (PDF, 9.6MB) Instructions for installing necessary python packages to run Local Client under Mac OS.

Local Client will check for any updates to itself or to the selected content database each time it runs.

Currently available databases are

  • PSLID RandTag Release 2 (GFP-tagged NIH 3T3 cell clones) (server name: lanec1web1.compbio.cs.cmu.edu)
  • Human Protein Atlas Confocal Immunofluorescence Image (server name: proteinatlas.org)
  • The Cell Library fluorescence microscopy images (server name: celllibrary.org)
  • Images used in the OMERO.searcher Nature Methods article (server name: omesplid2.compbio.cs.cmu.edu)
You (or your system administrator) can install OMERO.searcher Server on your local OMERO database server. This will permit you to be able to search within your database. Download OMERO.searcher Server v1.1.2
  • Unzip software and follow instructions in the README file. This will install the searcher on top of a previously installed database running OMERO 4.3.3.
  • You will need to ensure that the version of OMERO that you are running matches the version of OMERO.searcher.
  • You will have the option of setting up an External search page that will allow you (or others, if you permit) to search through your database for images that are similar to query images on their own computer (see item 1 above).

Archive of previous versions

Download OMERO.searcher v1.0

Acknowledgments

Development of OMERO.searcher has been supported by US National Institutes of Health grants GM075205 (R.F. Murphy, PI), EB008516 (K.W. Eliceiri, PI), and GM092708 (C.M. Kane, PI), and by grant 095931 from the Wellcome Trust (Jason Swedlow, PI).


Last Updated: 23 May 2014




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