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SCientific Image Format Input & Output: a flexible, extensible framework for image I/O. *EXPERIMENTAL* All API is subject to change, so depend at your own risk! See also @openmicroscopy/bioformats.

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SCIFIO

Join the chat at https://gitter.im/scifio/scifio

SCIFIO (SCientific Image Format Input & Output) is an extensible Java framework for reading and writing images, particularly N-dimensional scientific images.

This core package supports parsing pixels and metadata for a collection of open formats. Additional formats can be supported simply by downloading SCIFIO plugins and including them in your project.

Purpose

SCIFIO's primary purpose is to provide a clear convention for supporting image input and output. By lowering the barrier for adding new image formats, all SCIFIO-backed software will grow more versatile and powerful.

Supported formats

The SCIFIO core includes support for:

  • APNG
  • AVI
  • BMP
  • DICOM
  • EPS
  • FITS
  • GIF
  • ICS
  • JPEG
  • JPEG2000
  • MNG
  • Micro-Manager
  • NRRD
  • PCX
  • PGM
  • QuickTime
  • TIFF
  • Zipped images

Additionally, Bio-Formats is available as a SCIFIO plugin for supporting more than a hundred additional proprietary formats.

For users

ImageJ2 and Fiji use SCIFIO for image I/O.

For developers

Several software libraries use SCIFIO for image I/O:

  • SCIFIO has built-in support for opening and saving ImgLib2 data structures (see the io.scif.img package).
  • We have updated Bio-Formats to also support SCIFIO plugins, backwards compatibly with existing code.
  • ITK has an ImageIO module for reading and writing images using SCIFIO.

Developer documentation:

More information

For more information, see the SCIFIO FAQ and SCIFIO web site.

Getting help

SCIFIO uses the Image.sc Forum for support. Start a new topic tagged with scifio.

Contributing to SCIFIO

SCIFIO is an open project and anyone is very welcome to submit pull requests to the SCIFIO repository.

With SCIFIO's focus on extensibility, you typically will not need to make upstream changes to get your formats into users' hands. However, if you are interested in submitting a pull request, that's great! All we ask is that you check:

mvn clean test

from the top level.

If you're adding a new feature, it would be fantastic if you could write a unit test for it! Simply base it on JUnit to have it run by the SCIFIO test suite.

About

SCientific Image Format Input & Output: a flexible, extensible framework for image I/O. *EXPERIMENTAL* All API is subject to change, so depend at your own risk! See also @openmicroscopy/bioformats.

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