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You are here: Home Documentation OMERO v4.2.2 OMERO.analysis

Analysis Overview

OMERO supports analysis via a rich application programming interface (API), available currently in several languages: Java, C++, Python, and Matlab . These are the same APIs that both the desktop and web clients use to access your data when stored inside OMERO.

Local analysis

If you are interested in running your analysis locally and storing the results to the server, then your first step is to become familiar with the developer documention.

Distributed analysis via OMERO.scripts

Once you have your local analysis working, you can push it onto the server for background processing. For more information, see OMERO.scripts.

As of 4.2.0, your scripts must either be written in Python or be wrapped with a Python script.

Third-party analysis and OMERO.tables

Support has been added for some third-party analysis data, which gets converted in OMERO into a common format. These formats include:

  • MIAS data, measurements, and overlays
  • InCell data and measurements
  • Flex data with Acapella results (screencast). In the Flex case, additional configuration may be necessary for accessing both the raw data and the analysis results. See FlexSupport on the wiki for more information, or watch the configuration screencast.

The analysis results which are parsed out of the formats listed above are converted to HDF by the OMERO.tables API. This facility can then be used by clients to visualize the parsed measurements, and in the case of regions of interest, see their location overlayed on the associated image:

Other high-content screening (HCS) data

In addition to the Flex, Mias, and InCell 100 file formats, BD Pathway, Olympus ScanR, and native OME-XML/TIFF files files can all be imported as HCS data, though without support for any external analysis data which may be attached. If you are interested in having other analysis formats supported, contact either the open source community or Glencoe Software depending on your needs.

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