standalone

The Topology ToolKit (TTK) is an open-source library and software collection for topological data analysis in scientific visualization.

TTK can handle scalar data defined either on regular grids or triangulations, either in 2D or in 3D. It provides a substantial collection of generic, efficient and robust implementations of key algorithms in topological data analysis. It includes:
 · For scalar data: critical points, integral lines, persistence diagrams, persistence curves, merge trees, contour trees, Morse-Smale complexes, topological simplification;
 · For bivariate scalar data: fibers, fiber surfaces, continuous scatterplots, Jacobi sets, Reeb spaces;
 · For uncertain scalar data: mandatory critical points;
 · For time-varying scalar data: critical point tracking;
 · For high-dimensional / point cloud data: dimension reduction;
 · and more!

 

TTK makes topological data analysis accessible to end users thanks to easy-to-use plugins for the visualization front end ParaView. Thanks to ParaView, TTK supports a variety of input data formats.
 

TTK is written in C++ but comes with a variety of bindings (VTK/C++, Python) and standalone command-line programs. It is modular and easy to extend. We have specifically developed it such that you can easily write your own data analysis tools as TTK modules.

ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView’s batch processing capabilities.

ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of petascale size as well as on laptops for smaller data, has become an integral tool in many national laboratories, universities and industry, and has won several awards related to high performance computation.

Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline—modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.

The software FishInspector provides automatic feature detections in images of zebrafish embryos (body size, eye size, pigmentation). It is Matlab-based and provided as a Windows executable (no matlab installation needed).

The recent version requires images of a lateral position. It is important that the position is precise since deviation may confound with feature annotations. Images from any source can be used. However, depending on the image properties parameters may have to be adjusted. Furthermore, images obtained with normal microscope and not using an automated position system with embryos in glass capillaries require conversion using a KNIME workflow (the workflow is available as well). As a result of the analysis the software provides JSON files that contain the coordinates of the features. Coordinates are provided for eye, fish contour, notochord , otoliths, yolk sac, pericard and swimbladder. Furthermore, pigment cells in the notochord area are detected. Additional features can be manually annotated. It is the aim of the software to provide the coordinates, which may then be analysed subsequently to identify and quantify changes in the morphology of zebrafish embryos.

IDE for JVM

Every aspect of IntelliJ IDEA is specifically designed to maximize developer productivity. Together, the powerful static code analysis and ergonomic design make development not only productive but also an enjoyable experience.

It can be seen as an alternative to Eclipse for example for java based development. It exists in both a commercial and a free and open source version.