The software we want to share this week is really neat - here we present Social-Evolution-and-Behavior/anTraX!
The image above comes directly from the arXiv supplementary material publication from the authors. You can probably guess from the above what the software does - we are tracking ants (or other small friends) to better understand their movement or behavior. Are you already familiar with this software? We encourage you to contribute to the research software encyclopedia and annotate the respository:
otherwise, keep reading!
From the authors, anTraX is:
high throughput tracking of color-tagged insects
It seems like the authors had ants (or other small insects) that were tagged with colored dots, and wanted a simple approach to be able to track them. I’d imagine they are studying colony movement or behavior over multiple days, and needed a good way to keep track of movement. The software works with Linux and (optionally) Matlab, and even includes a test dataset with the Getting Started guide if you don’t have your own ants and want to play around with it anyway.
You can read the paper on arXiv (and browse to the figures section to see a whole set of cool videos like the one above!) or on eLife.
@article {10.7554/eLife.58145,
article_type = {journal},
title = {anTraX, a software package for high-throughput video tracking of color-tagged insects},
author = {Gal, Asaf and Saragosti, Jonathan and Kronauer, Daniel JC},
editor = {Berman, Gordon J and Dulac, Catherine and Shaevitz, Joshua W and Perez-Escudero, Alfonso},
volume = 9,
year = 2020,
month = {nov},
pub_date = {2020-11-19},
pages = {e58145},
citation = {eLife 2020;9:e58145},
doi = {10.7554/eLife.58145},
url = {https://doi.org/10.7554/eLife.58145},
abstract = {Recent years have seen a surge in methods to track and analyze animal behavior. Nevertheless, tracking individuals in closely interacting, group-living organisms remains a challenge. Here, we present anTraX, an algorithm and software package for high-throughput video tracking of color-tagged insects. anTraX combines neural network classification of animals with a novel approach for representing tracking data as a graph, enabling individual tracking even in cases where it is difficult to segment animals from one another, or where tags are obscured. The use of color tags, a well-established and robust method for marking individual insects in groups, relaxes requirements for image size and quality, and makes the software broadly applicable. anTraX is readily integrated into existing tools and methods for automated image analysis of behavior to further augment its output. anTraX can handle large-scale experiments with minimal human involvement, allowing researchers to simultaneously monitor many social groups over long time periods.},
keywords = {ants, social insects, collective behavior, ethology, social behavior, formicidae, tracking, machine vision, machine learning},
journal = {eLife},
issn = {2050-084X},
publisher = {eLife Sciences Publications, Ltd},
}
There are many resources available for learning!
or read more about annotation here. You can clone the software repository to do bulk annotation, or annotation any repository in the software database, We want annotation to be fun, straight-forward, and easy, so we will be showcasing one repository to annotate per week. If you’d like to request annotation of a particular repository (or addition to the software database) please don’t hesitate to open an issue or even a pull request.
You might find these other resources useful:
For any resource, you are encouraged to give feedback and contribute!