ITKv4 & V3D Plugins

Following the initiative of improving ITK’s support for Microscopy applications that we outlined in a previous post,
we have been developing ITK plugins for the V3D application.

V3D is an application for visualization and analysis of biomedical images developed by the Howard Hughes Medical Institute at the Janelia Farm campus http://penglab.janelia.org/proj/v3d.

It is cross platform (Linux, Mac and Windows) and it is typically used in:

  • Cell segmentation
  • Neuron tracing
  • Brain registration
  • Annotation
  • Quantitative measurement and statistics
  • Data management

Other V3D resources are hosted at NITRC http://www.nitrc.org/projects/v3d/

These new ITK plugins are, of course, Open Source, and are available under an Apache 2.0 License  at the github repository: ITK-V3D-Plugins.

The ITK plugins for V3D cover, among others, the following functionalities

  • Intensity Transformations
  • Mathematical Morphology
  • Level Set segmentation
  • Region Growing segmentation
  • Label Map processing
  • Rigid and Affine Registration
  • Demons Deformable Registration
  • Object counting and measurement statistics
  • Distance maps
  • Statistical Classifications
  • Edge Detection
  • Watersheds
  • Smoothing
  • Arithmetic operations
  • Binary operations

The development of ITK plugins for V3D serves two purposes

  • Exposing ITK functionalities to researches who analyze microscopy data
  • Uncovering the areas in which ITK requires improvements in order to better serve the microscopy community.

Both of them are of particular interest for the development of ITKv4.

We welcome your feedback on the implementation and usability of these plugins, and of course, encourage you to join the development team if you have an interest in microscopy image analysis.

Questions or comments are always welcome!