ImgLib2 support for ClearVolume

This repository contains

• all functionalities to bridge from loaded imglib2 image containers to ClearVolume.
• a ImageJ2/Fiji plugin that embedds ClearVolume in a usable way.
• the user interface can also be used in other contexts, e.g. as a viewer plugin in KNIME.

You would like to see the final plugins that rely on this repository?

Sneak peak at the GUI in Fiji/ImagJ2:

The TableCellViewer plugin in KNIME:

You would like to use ClearVolume plugin in Fiji/ImageJ2 or KNIME?

• Two hoops that will fall away soon but currently have to be taken:
  • Fiji must be started using Java 1.7 or 1.8 (or later?). See these instructions.
  • Fiji must use the ImageJ2 data structures (imglib2). Enable in Fiji with 'Edit - Options - ImageJ2...'.
• Install ClearVolume plugin directly in Fiji:
  • Help - Update...
  • click 'Manage Update Sites'
  • check 'ClearVolume' in list of update sites and close window again.
  • update installs, done!
• Knime installation instructions can be found here.

You would like a superficial explanation of how it all works?

Since ClearVolume can, to date, only show images stored in native byte arrays we need to translate imglib2 image container to native byte type images. While this is ok for 8bit images, 16bit images are represented as arrays of type short in imglib. Here you find two things that enable you to display every RealType image container coming from imglib2 into ClearVolume:

• ClearVolumeUnsignedShortType -- a alternative 16 bit short type image type implementation that uses a native byte array to store voxel intensities. An image that is loaded into any imglib2 container using a image factory with this new type can directly be shown in ClearVolume using static methods in class ClearVolume.
• For any other imglib2 container we offer the converter RealClearVolumeUnsignedShortConverter. Feel free to use this converter just as any other imglib2 converter, but we do also provide static convenience methods in class ClearVolume.