SciScan 1.1 software incorporates the OME XML and TIFF formats

The HyperScope multiphoton imaging system now has advanced imaging capabilities; the introduction of an extended wavelength lens set means you can image deeper and through thin scattering layers in in vivo samples. Learn more here.

SciScan 1.1 software OME compatible


The next major release of Scientifica’s multiphoton acquisition software, SciScan, will incorporate the Open Microscopy Environment’s XML and OME-TIFF formats. This provides a new option to load, organise and analyse data with the Bio-Formats Java library while maintaining full backwards compatibility with existing analysis routines (e.g. in Matlab, Python, ImageJ).

The Open Microscopy Environment (OME) is a consortium of academic laboratories and commercial entities that create open tools to support the data management of biological light microscopy. Funding for the OME comes from the Wellcome Trust Strategic Award and BBSRC.

They have created the OME Model, a specification for storing biological imaging data including a wide variety of picture, acquisition and experimental parameters. This enables the simple exchange of imaging data between different software packages.

Co-founder of the OME, Professor Jason Swedlow, said: "The OME Consortium is quite excited that Scientifica now supports OME-XML and joins the growing number of entities that use OME’s tools to promote the open exchange of and access to scientific imaging data.”

What does this mean for you?

There are two different file formats associated with this model. OME-XML is a file format used to store metadata according to the OME model in an XML file that can be shared easily between different sites and users. OME-TIFF is a multi-page tiff file that contains the OME metadata within the header as OME-XML. The pixels of the OME-TIFF file can be read by any TIFF-compatible programme, and the metadata can be extracted with an OME-aware application.

The ability to save imaging data in SciScan as an OME-TIFF or with an OME-XML file allows users to open, organise and share metadata in a fully standardised format. This helps researchers to disseminate and analyse data in other software, compare their data with others using the OME Model and keep track of where and how the images were acquired.

The OME consortium currently has two major tools to help those working with OME-XML and OME-TIFF files:

  • Bio-Formats is a library containing many features related to OME-XML, including conversion of third party metadata into the OME-XML structure.
  • OMERO server can import OME-XML and OME-TIFF data and export OME-TIFF files.

To learn more about the OME Model and formats visit the Open Microscopy Environment website.

Scientifica SciScan Software

Award-winning two-photon acquisition software designed and built by Scientifica in collaboration with researchers.

Control both galvo and resonant scanning systems for both in vivo and in vitro imaging applications.

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