ImageJ

We are happy to announce the first stable release version of the ImgLib2 core library!

This release was a central goal of the recent hackathon at LOCI in Madison, during the week of October 13 - 17.

The ImgLib2 core library is now available on Maven Central, and the source code for all ImgLib2 projects is accessible on GitHub.

Like the SciJava and ImageJ2 projects, ImgLib2 releases now follow the semantic versioning scheme. Also, the project and git repository structure has changed. The main imglib repository has been split into multiple repositories, named consistently with the artifact names and java package prefixes. Projects are now coupled using non-SNAPSHOT versions, in order to achieve reproducible builds.

For further technical details on project structure, see the Architecture page.

Before coming out of beta, we have made several last-minute changes to the code:

• All @Deprecated methods and classes have been removed.
• All metadata handling (formerly imglib2-meta subproject) is being moved into imagej-common. From ImgLib2 core, the classes AnnotatedSpace, AbstractAnnotatedSpace, and Axis were moved to imagej-common.
• The current ROI representation was not considered stable enough to be included in a release. The net.imglib2.roi and net.imglib2.labeling packages were moved to the new imglib2-roi subproject which will remain in beta for now.
• The net.imglib2.multithreading package was moved to imglib2-algorithm and deprecated.
• We merged work by Albert Cardona and Stephan Preibisch on "fractional" types. ImgLib2 NativeTypes map pixels into primitive arrays, where often the mapping is one-to-one. For example, an UnsignedByteType pixel maps into one byte of a primitive byte[] array. With fractional types this mapping maybe non-integral, for example Unsigned12BitType maps pixels into a long[] array, where each pixel occupies 12/64 longs.
• Superfluous generic parameters were removed from Projector<A,B> interface which is now only Projector. Projector implementations were fixed accordingly.
• Several classes were renamed or moved to more suitable places:
  • Extended[Real]RandomAccessibleInterval moved to the net.imglib2.view package.
  • RandomAccessibleOnRealRandomAccessible moved to the net.imglib2.view package.
  • Binning moved to the net.imglib2.util package.
  • The contents of package net.imglib2.collection (KDTree etc.) moved to the net.imglib2 package.
  • net.imglib2.concatenate.Util was renamed to net.imglib2.concatenate.ConcatenateUtils.
  • Bounded moved to the net.imglib2.outofbounds package.
  • The class NearestNeighborInterpolator from package net.imglib2.interpolation.neighborsearch was renamed to NearestNeighborSearchInterpolator (to avoid confusion with the net.imglib2.interpolation.randomaccess.NearestNeighborInterpolator class).
  • The Pair interface moved to the net.imglib2.util package.
• The net.imglib2.util.Util class was cleaned up:
  • Methods getTypeFromRandomAccess() and getTypeFromRealRandomAccess() were removed. We considered them too dangerous because the RandomAccess may be pointing to invalid position.
  • Unused methods setCoordinateRecursive() and getRecursiveCoordinates() were removed.
  • Some variants of computeLength() and computeDistance() were removed. Use methods distance() and length() from net.imglib2.util.LinAlgHelpers instead.
  • Methods computeMedian(), computeAverage(), etc. were renamed to median(), average(), etc.
• These unused classes were removed:
  • IterableIntervalSubsetT
  • Triple
  • RealPositionableFloorPositionable
  • RealPositionableRoundPositionable
  • ImgTranslationAdapter
• Packages net.imglib2.img.constant and net.imglib2.sampler.special were removed (ConstantImg, ConstantRandomAccessible, etc). Similar functionality can now be achieved through the net.imglib2.util.ConstantUtils class and Views.

All ImgLib2 subprojects have been adapted to these changes and released (in some cases as new beta versions).

One thing still pending is to upload these new ImgLib2 releases to the ImageJ and Fiji update sites, making them available to users of ImageJ and Fiji. This change has been rather involved, since there is a lot of downstream code affected by the API changes. But we expect to make the new ImgLib2 available to users before the end of the calendar year. Stay tuned for further announcements!