Algorithms and Software


Highlighted Software

TubeTK is an open-source toolkit for the segmentation, registration, and analysis of tubes and surfaces in images.

Tubes and surfaces, as generalized 1D and 2D manifolds in N-dimensional images, are essential components in a variety of image analysis tasks. Instances of tubular structures in images include blood vessels in magnetic resonance angiograms and b-mode ultrasound images, wires in microscopy images of integrated circuits, roads in aerial photographs, and nerves in confocal microscopy.

A guiding premise of TubeTK is that by focusing on 1D and 2D manifolds we can devise methods that are insensitive to the modality, noise, contrast, and scale of the images being analyzed and to the arrangement and deformations of the objects in them. In particular, we propose that TubeTK's manifold methods offer improved performance for many applications, compared to methods involving the analysis of independent geometric measures (e.g., edges and corners) or requiring complete shape models.

TubeTK is implemented as a C++ library and makes extensive use of ITK and VTK. Select methods of TubeTK are provided as command-line applications and python functions.

ParaView Glance is a light-weight, open-source, web application developed at Kitware for visualizing volumetric images, molecular structures, geometric objects, and point clouds.

As part of the ParaView platform, it is intended to allow users to quickly glance at their small to medium size data. Ultimately, ParaView Glance is intended to help you:

    1. Quickly view your data on your computer. It launches quickly and supports a wide variety of data formats so that you can quickly look at the most recent results from a new algorithm you are developing or visually confirm the contents of a data file on your drive.

    2. Review items-of-interest on Girder. Imagine that you have reviewed a large collection of data on Girder, and you have narrowed your search to two interesting items that you want to explore more closely. Via an optional Girder module, ParaViewGlance can be associated with appropriate types of data items and launched to download and view items of interest with minimal interaction (a single click per item), minimal delay (requiring only the time to transfer the data to your machine), and no need to explicitly install an application or run a dedicated server (ParaViewGlance is a stand-alone, JavaScript+WebAssembly application).

    3. Develop new applications involving VTK.js and ITK.js. ParaView Glance has been architected to be a highly customizable platform. It can be used as a basis for creating stand-alone web-based applications, desktop applications via Electron, and web-based systems that involve services from ParaViewWeb and/or Resonant.