Tron Machine Information Guide
TRON Machine: TRacking Overlapping Neurons
Programmed by Justin Carrington. It's all his fault.
Designed by Justin Carrington and Russell Taylor, with additional help from Kendra Taylor and Erik Dent. Special thanks to the Dent Lab and community at the University of Wisconsin-Madison for support in creating this software. The Hilldale Undergraduate Research Fellowship played a large role in funding Justin's work for this project.
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, thru techniques including erosion, Gaussian blur, and thresholding, 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.
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