Cytometry Development Workshop
Carnegie Mellon University
Lane Center for Computational Biology
Center for Bioimage Informatics
Biological Sciences Department
Biomedical Engineering Department
Machine Learning Department
Murphy Lab - Software - OMERO.searcher
||Local Client updated!
Now able to search against your own content database using your own feature calculation code.
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
- Additional public databases will be made available shortly (a list of links to these databases will be available here). These will include
- the subset of images from The Cell library that are 2D or 3D fluorescence microscope images.
- the full Release 2 of the RandTag project.
- 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.
Local Client v1.2
- 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
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
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).