On April 3, 2014, inviCRO officially released VivoQuant 1.23. Following the release, two webinar’s were held to review the new and improved features in VivoQuant 1.23. All materials covered and recordings of the webinars are available.
With the release of VivoQuant 1.23, new functionality has been added to facilitate iPACS communication within VivoScript. Users are now able to easily filter though entire iPACS projects easily and pick out the desired data sets in clean, simple scripts. The functionality has been written in VivoScript and included in every new install of VivoQuant 1.23 as ipacs.vqs, so implementing it within your VivoScrips is very easy.
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.
The iPACS reporting engine is a powerful tool to access iPACS’ object relational database (where for instance projects, patients, studies, datapoints, study planner events, etc… are stored) as well as the file-based WebDisk and export the data in for instance PDF, Excel Spreadsheets, CSV, plain text, XML, etc… In this example I would like to show a small example on how to export the projects table in form of a native Excel spreadsheet, including links and formats.
With iPACS 1.07 the Dashboard was introduced, which allows the user to configure their own front page and thus get access to all the information they actually need right after login. The Projects dashboard widget is designed to ease navigating through huge (500+) project trees with quick access to important project information as well as the Image/DICOM Browser and the file-based WebDisk. Also available are widgets for a world clock, the current jobqueue, messages, events from the Study Planner, last accessed projects and directories and many more…
This example will further explore using VivoScript libraries by adding three more functions and then dive into co-registering two images (using one of these functions) and applying some a image arithmetic, in this case calculating the relative difference.
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.
In this section we are having a look at how to extract meta information from studies in a project and writing them to a local text file. The looping through all studies of a project is described in Part I of this introduction.
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.