Software

Disclaimer: I never received any formal training, like completely zero, in coding or programming. I am self-taught, have had some very helpful mentors, guides, and collaborators, and early on I figured out how to search the internet for solutions. If you want to learn more or get started, there are a lot of excellent free resources. I now try to pass those skills on to my students, and maintain open-source access to everything I do.

Hopefully something is helpful to you.

3D video analysis

Argus – 3D video analysis software

Argus is a python application that provides 3D video analysis tools for lab and consumer grade cameras. We designed it to allow use of non-synchronized cameras with high-distortion lenses (e.g. GoPro) in challenging field situations (or the backyard), but it also works with lab-quality cameras. The files are completely interchangeable with the MATLAB-based DLTdv set of digitizing tools. Get the paper, and go visit the program page for usage and installation instructions. NOTE: as of 2025-04-23, updates to Argus in in progress to modernize it. See my GitHub page for the latest verision that works on macOS. There may be errors in Clicker on Windows.

I have written some other minor functions to help with analysis of data and production of videos for presentation. If you use Argus, please feel free to contact me directly for help with either!

DLC2DLT2DLC – Convert to and from deeplabcut format

Argus (above) and DLTdv use direct linear transformation (DLT) to perform 3D reconstruction with multiple cameras, and save data in a specific format. DeepLabCut automates the landmark digitizing process – the most cumbersome part of high-speed video analysis. While DeepLabCut has 3D capabilities, it relies on a checkerboard calibration that may be difficult to perform in the field. This set of python scripts allows the user to use Argus’ or EasyWand’s wand calibration for 3D calibration and to label training data, then convert to DeepLabCut format for training and individual video analysis, and then convert back to Argus or DLTdv for final 3D reconstruction.

Classroom Related Software

Text-to-quiz for Canvas LMS – Convert text to QTI for Canvas quiz import

Writing quizzes in Canvas is a tedious task. There is an expensive program to covert a Word document to a Canvas quiz, but it works only on Windows. This program will convert a simply formatted text document to a QTI (zip) file that can be easily imported to Canvas to add the questions to a question bank. It works with all the question types in Canvas’ “New Quizzes”, and now runs as a pre-packaged app (or command line). Installation and usage instructions are available on the package’s GitHub page.

Lab Practical Exam Generator – Generate lab practical exams

This program is designed to help generate lab practical exams for anatomy and physiology or other lab courses. It allows instructors to have a database (or pool) of “materials”, with the idea that there could be multiple labels per item, and mutlple questions per label. The database is stored in an excel file for easy editing and sharing among instructors. An instructor can then assign materials to “stations” and select among available questions per station. It then outputs formatted answer sheets and keys, a “set up” file to guide settign up the exam itself. This can be used to relatively easy make differnet versions of an exam based on the same material set up to reduce cheating within and among lab sections.

NOTE: as of 2025-04-23 it is currently in testing phases, but please contact me if you are interested in using it. The program can be run as a command line or GUI application. Installation and usage instructions are available on the package’s GitHub page