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scifio / scifio-lifesci

SCIFIO plug-in providing support for proprietary life science formats (e.g. those supported by Bio-Formats).
GNU General Public License v2.0
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Clarification about the goal of scifio-lifesci #3

Closed hadim closed 10 years ago

hadim commented 10 years ago

Only to be sure the goal of scifio-lifesci is to replace bioformats in the future.

So it's a scifio plugin for all formats supported by bioformats (except OME XML which already add its own plugin ome-formats) ?

And the goal of scifio-bf-compat is to make a kind of bridge between scifio and bioformats until scifio-lifesci is ready for production ?

Am I correct ?

hinerm commented 10 years ago

So it's a scifio plugin for all formats supported by bioformats (except OME XML which already add its own plugin ome-formats) ?

Yes, but specifically scifio-lifesci is intended for SCIFIO implementations of the proprietary readers supported by Bio-Formats, and could also contain life science image formats not currently supported by Bio-Formats.

OME-TIFF is an "open exchange" format. It was designed to be open source and capable of representing a wide variety of data models via OME-XML. This allows standardization of image formats by translation to OME-TIFF.

So ultimately the goal of scifio-lifesci is both to implement SCIFIO formats for the proprietary Bio-Formats readers, and to provide explicit Translator implementations for converting the metadata of those formats to OME-TIFF (which happens implicitly in Bio-Formats).

These are the two fundamental types of SCIFIO plugins we had in mind: open exchange formats, and proprietary libraries which convert to those open formats.

And the goal of scifio-bf-compat is to make a kind of bridge between scifio and bioformats until scifio-lifesci is ready for production ?

Essentially, this is correct.

hadim commented 10 years ago

Thank you for the clarification. I close it !

ctrueden commented 10 years ago

To clarify matters further: scifio-lifesci is a placeholder for life sciences formats that have been ported from the Bio-Formats API to the SCIFIO API, as well as a place to put new life science file format implementations in the medium term. The eventual goal is for Bio-Formats to continue to provide complete support for life science file formats, but built on top of the SCIFIO core library.

For further details, see How is SCIFIO related to Bio-Formats? in the SCIFIO FAQ.