Learning to use DeepLabCut
Created on Tue Nov 17 2020 17:37:13 GMT+0000 (Coordinated Universal Time)
flow diagram on learning DLC
Learn to use DeepLabCut!
Welcome to the DLC Course! Ready to get started?Here, we will walk you through the main steps to get DLC up and running in your hands in no time! You can start at the top, or jump to any topic you might want to learn more about!
Got Poses? Now what?
Scaling up your analysis pipeline
Step 3: you've got a network, now let's evaulate it's performance
A deeper dive into neural network selection
Step 2: using DeepLabCut on your own data
Learning more about DeepLabCut!
Jumping deeper into Python: resources, more links, and #proTips
Step 1: getting set up with python, anaconda, and your dlc computing environment
We have 4 key papers that help you learn how it works, and how best to use DLC!Mathis et al,Nature Neuroscience 2018or free link:rdcu.be/4RepNath*, Mathis* et al,Nature Protocols 2019or free link:https://rdcu.be/bHpHNMackenzie W. Mathis& Alexander Mathis.Deep learning tools for the measurement of animal behavior in neuroscienceCurrent Opinion in Neurobiology Volume 60, February 2020, Pages 1-11Alexander Mathis, Steffen Schneider, Jessy Lauer, Mackenzie W Mathis -A Primer on Motion Capture with Deep Learning: Principles, Pitfalls, and PerspectivesNeuron 2020. https://doi.org/10.1016/j.neuron.2020.09.017
You can automate your pipelineUsing tools like cron jobs, batch processing, DataJoint, AWS, and more, we point you to the tools that can help make your life even easier ....
Typically the first step is to locally install DeepLabCut on your computerYou can install just for CPU use (i.e., for labeling data), or if you have your own GPU, you can install for this as well. Otherwise, you can use free cloud services, such as google colab! Click away to read more ....
Looking for a deeper dive into Python?There are a lot of amazing resources, jump in here!
How do the neural networks work? How do I best pick a network for my use case?DeepLabCut has several modified neural networks for you to choose from. The powerful ResNet-50, -101, the ultra fast MobileNetV2s, and now EfficientNets, bringing you the latest high performance.Read our paper on comparing these networks:https://arxiv.org/abs/1909.11229And #DLCProTips on what you might want to use:https://github.com/DeepLabCut/DeepLabCut/wiki/What-neural-network-should-I-use%3FDeepLabCut/DeepLabCutTL;DR - your best performance for most everything is ResNet-50; MobileNetV2-1 is much faster, needs less memory on your GPU to train and nearly as...GitHub
Your network is only as good as your input data, and of course how you load that data and train it. We provide several tools to evaluate your network, so you can carry on with confidence in your video analysis.
Need help with your own project?There is an active user forum:https://forum.image.sc/tag/deeplabcut
There are many new packages that take in the outputs of DLC for you to do further analysis!
Contact DevelopersGitHub / Twitter / Youtube
There are many ways to use DeepLabCut: through a full GUI (NO programming required), via. Jupyter Notebooks, or in the command line interface! We have created video tutorials for each of these options:https://www.youtube.com/channel/UC2HEbWpC_1v6i9RnDMy-dfADeepLabCutEnjoy the videos and music you love, upload original content, and share it all with friends, family, and the world on...YouTube
We post new code release announcements on Twitter (please follow!), and well as #DLCProTips! Search for more details...
Did you know, we have several review papers on deep learning for animal behavior! Some cover the current state of the field, while others are deep dives into the technology, and how best to use them!
You should check out our new paper, which really takes you into important points on neural network selection, data augmentation, and pitfalls to avoid! https://www.cell.com/neuron/fulltext/S0896-6273(20)30717-0open source:https://arxiv.org/abs/2009.00564
We have a code and pointers to other packages that will help you analyze the output of DLC!https://github.com/DeepLabCut/DLCutils
If you want to make your own customize analysis pipeline, check out:https://scikit-learn.org/stable