Easy guide to use DeepLabCut on Bowdoin's HPC

This page belongs to the lab of Professor Hadley W. Horch at Bowdoin College. All of her behavioral data, along with DeepLabCut information and user guide are centralized in this GitHub location.

For actual guide on how to use DeepLabCut on Bowdoin's HPC, please refer to Getting-started-DLC.md. Click here to go to the guide.

Want to use existing HPC scripts for your DLC project? Read the section on HPC_Scripts for more information.

References

1. Steps on how to get started using DLC on the HPC (Getting-started-DLC.md)
2. The R scripts and Python files necessary to do so (HPC_scripts)
3. Extensive videos & data on cricket behavior (negative phonotaxis) (Hidden by .gitignore)
4. DLC examples on cricket negative phonotaxis (Hiddnen by .gitignore)
5. DLC and HPC troubleshooting information (Additional_DLC_Help/*) Some of the information is outdated, but still useful for reference.

Reference to DLC's official github. Reference to the original R script in 2019.

(Deprecated) Link to Tom's forked repository. Some leftover half-finished projects are still going and will be eventually merged back into this repository.

HPC_scripts/*

Scripts that can be used on Bowdoin's SLURM-based HPC Grid for DeepLabCut tracking.

The scripts are designed to work with DLC 2.3.9/2.3.10. As of Jun 2024, the corresponding DeepLabCut version is only installed in the new HPC. So instead of submitting a job on slurm (with ssh slurm.bowdoin.edu), submit those jobs on moosehead (with ssh moosehead.bowdoin.edu). Everything else (sbatch...) should be the same.

To use these scripts:

1. Clone this repository to your HPC folder. Alternatively, download the folder and put it to your HPC/microwave folder.
2. Change neseccary parameters in the scripts. Most importantly, the path config.yaml file and paths to your videos.
3. When submitting a job with sbatch, you don't need to add -p gpu ... because the script would request the GPU for you.
4. :D

DLC_output/*

Hidden files (unpublished data), .csv (comma-separated file) outputted from DeepLabCut.

R files/*

Post-DLC processing. Visualizing and analyzing movements of the crickets. (This part is Cricket/G. bimaculatus specific).