On November 28, 2016, inviCRO officially released VivoQuant 3.0. The updated version includes an extensive upgrade to the Modeling operator for Tracer Kinetic Models, new tools for filing Electronic Case Report Forms (eCRFs), flexible data selectors throughout the software, and 3D ROI Tool improvements.
On November 13, 2015, inviCRO officially released VivoQuant 2.5. The updated version includes a brand new fully-flexible Multi View, with expanded and enhanced data viewing options. Data interaction has also been enhanced with an increase in size of the display window and added support for zooming/panning within an image. VQ 2.5 also supports the newly updated modeling tool with more models than previously included, as well as the addition of voxel-wise modeling for parametric map generation.
On February 25, 2015, inviCRO officially released VivoQuant 2.0. The new version included a large User Interface re-design, with new buttons, menus, and and a more workflow-oriented look and feel. Also hightlighted was the new RGB viewer for viewing 2D and 3D RGB data alongside the standard 3D data VQ users are used to.
At inviCRO we strive to deliver software in accordance to highest scientific and quality standards. As a consequence, testing our software has become an integral part of the development process. In particular we follow a continuous integration process that allows us to keep our software working at most times and to detect and fix bugs very quickly. Additionally, with test-driven development we are continuously expanding our testing library and improving the quality of our software one test at a time.
A new VivoScript will be available with the release of VivoQuant 1.23: the Onion Tool. This tool allows the user to select a Region of Interest that he or she has segmented, and perform layer-based analysis. The tool operates on any ROI present in the 3D ROI Tool, and is configurable to fit your specific analysis needs.
Histogram based auto-thresholding (based on Otsu’s algorithm) is a great way to automatically segment two Gaussian distributions of values, e.g. background vs. animal. In this post we are looking into automating this process and placing the segmentation function into a library file so it can be reused in other scripts.
You can now find various VivoQuant generated movies in inviCRO’s new YouTube channel at http://www.youtube.com/invicro. If you subscribe to the channel you will be notified of new uploads. In this blog here you will then find additional information about how the movies where created.
For instance, you might want to checkout our VivoScript Introduction, which will also cover image and movie generation in later lessions.
In this post, I would like to show an example of how to iterate through all the patients of a project on an iPACS system using a VivoScript. This can for instance be useful for the automation of pre-processing data, or two produce quality control images for an entire project. The looping technique shown here will be used in subsequent tutorials, so this is the best starting point to get familiar with VivoScript.
Sometimes it is useful to be able to start external programs from within VivoQuant. VivoScript provides a function for this:
VQ.startTool("ProgramName"); VQ.startTool("ProgramName", baseDir, parameterList);
with ProgramName being a pre-configured name of the tool to start (see below on how to add your own tools), while the optional baseDir defines the current working directory the tool is started in. Finally, the parameterList is an array of optional parameters passed into the tool from the command line. Depending on the tool you are using such parameters could be used to for instance pass in files to the new tool.