This is a repo for high-throughput worm tracking in the Leifer lab. The -new repo is edited to track worm behavior in the odor flow chamber, characterizing chemotaxis behavior in a large arena.
The pipeline is used to process raw recordings of C. elegans navigation behavior, as published in: eLife2023;12:e85910 DOI: https://doi.org/10.7554/eLife.85910 (Continuous odor profile monitoring to study olfactory navigation in small animals. Chen, Wu, et al. 2023.)
Use Labview vi in LabviewVIs folder to run experiments in real-time. For the full odor navigation project, please check repo https://github.com/GershowLab/OdorSensorArray for control and communication with other devises. In the LabviewVIs folder, run gaussian correlation time.vi for recording or white-noise optogenetic stimuli. Run array_light_mix.vi to deliver optogenetic impulse.
Use the Bash scripts to submit the analysis pipeline to the computing cluster Della at Princeton. Specifically, use cluster_run.sh to run all or ProcessExperimentatDirectory.sh to run a specific data folder.
Use View ExperimentDirectory.sh to check the experiment files and use cluster_view.sh to check currently running jobs.
Use functions in the debuggingTools folder to plot images. Double check with the parameters.csv spreadsheet for tracking and devise parameters.
Use scripts in TrackAnalysis folder to identify behavioral modes along the worm track. For further analysis, please check repo https://github.com/GershowLab/OdorSensorArray with scripts in matlab_data analysis to analyze chemotaxis behavior.
If you use the design files and/or codes provided in this repository, please cite:
Kevin S. Chen, Rui Wu, Marc H. Gershow, Andrew M. Leifer. (2023). Continuous odor profile monitoring to study olfactory navigation in small animals. eLife. DOI: https://doi.org/10.7554/eLife.85910
Design files and codes provided in this repository are free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
This repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.