Python

Luigi is a Python module that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow management, visualization etc. It also comes with Hadoop support built in.

The purpose of Luigi is to address all the plumbing typically associated with long-running batch processes. You want to chain many tasks, automate them, and failures will happen. These tasks can be anything, but are typically long running things like Hadoop jobs, dumping data to/from databases, running machine learning algorithms, or anything else.

vmtk is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels.

vmtk is composed of

• C++ classes (VTK and ITK -based algorithms)
• Python classes (high-level functionality - each class is a script)
• PypeS - Python pipeable scripts, a framework which enables vmtk scripts to interact with each other

SuRVoS: Super-Region Volume Segmentation workbench

A volume is first partitioned into Super-Regions (superpixels or supervoxels) and then interactively segmented by the user providing training annotations. SuRVoS can then learn from and extend the annotations to the whole volume.

The ultimate goal of the NET framework is to make images of networks processable by computers. Therefore we want to have a pixel based image as input, as output we want a representation of the network visible in the image that retains as much information about the original network as possible. NET achives this by first segmenting the image and then vectorizing the network and then extracting information. The information we extract is

• First and foremost the graph of the network. We find the crossings (nodes) and connections between crossings (edges) and therefore extract information about the neighborhood relations, the topology of the network.
• We also extract the coordinates of all nodes which enables us to embed them into space. We therefore extract information about the geometry of the network.
• Last but not least we track the radii of the edges in the extraction process. Therefore every edge has a radius which can be identified with its conductivity.

In the following we will first provide detailed instructions on how to install NET on several platforms. Then we describe the functionality and options of each of the four scripts that make up the NET framework.