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Usage

The program takes microscopy image stacks as input and then identifies neurons in these images using image processing techniques. Some parameters for these methods can be modified. We are currently working on providing users more control over these methods to make the software robust. After initial pre-processing, an algorithm is used to identify 3D objects (neurons). The system is not perfect so we have incorporated the ability to add and remove neurons which were incorrectly identified by the counter. Following identification of neurons in an image, the migration (from a region drawn by the user) is measured. An Excel file is produced containing the positions of neurons in images and their migration. In addition, images are generated which show the location of the neurons which are quantified.

The processing algorithms are largely based off plugins for Fiji, an open source image processing package based off of ImageJ but has been adapted to increase efficiency. However, this standalone software does not require Fiji in order to run. Like Fiji, this software is also open-source. This means that we permit (and encourage!) others to use and modify our work to make it a better tool for the scientific community.

History

The program was originally created by Justin Carrington for use in the Dent Lab in order to analyze neuronal migration in microscopy images of mouse brains in May of 2018. Justin is currently the sole developer for the project, but collaboration with graduate students in the Dent Lab––namely Russell Taylor––has allowed it to be a success. The program was designed for personal use but we have realized that it could prove a useful tool for other researchers in the field of neuroscience. With this in mind we have made changes such that the program can be applied beyond our own research.

We have reached a point of stability with recent builds, but the software is still undergoing frequent and large changes to improve functionality. If you are to use this software, understand that it is not perfect: there are bugs. We're working through them. This project is not our sole focus and we cannot guarantee that every build will work exactly as intended. You can do us a great service by lettings us know when components of the program are failing. You can email the developer, Justin Carrington (Undergraduate), at justincarrington2000@gmail.com or Russell Taylor (Graduate Student) at rjtaylor@wisc.edu.

The Tron Machine is in its infancy but we are revolutionizing neuronal analysis techniques. Traditionally, neurons are hand-picked in images and their migration is hand-drawn and calculated. Our system reduces inherent biases involved with this approach. The Tron Machine simultaneously cuts back on analysis time through automation. Implementing computational analysis into neuroscience research is an exciting development of the 21st century. We hope you join us on the journey.