alexemg / dlc-cajal-course

Course materials for the Modern Methods for Quantifying Behavior Course!

Modern Methods for Quantifying Behavior

Dear participants, welcome 🙌 to the 2023 edition of the hands-on Neuroscience course Modern Methods for Quantifying Behavior

Here you will find all the course material 📚 you will need to complete your project.

Teaching Team for the second edition, anno 2023 🏆

Role 🔥	Name 📛	Hub 🗺️📍	GitHub 🛠️	Twitter 🐥
Co - Director 🎖️	Alexander Mathis	Geneva (CH)	GitHub	@TrackingPlumes
Co - Director 🎖️	Danbee Kim	🛰️ online	GitHub	@taunbot
Cajal Administrator 📝	Elena Drosti	🛰️ online
Teaching Assistant 🦅	Sofia Minano	London (UK)	GitHub	@SofiMinano
Teaching Assistant 🦇	Jonas Håkansson	🛰️ online	GitHub	@ScientistJonas
Teaching Assistant 🐭	Andrada Marica	🛰️ online	GitHub	@andrada_marica
Teaching Assistant 🐭	Sabrina Benas	Buenos Aires (ARG)	GitHub	@Sabrineiitor
Teaching Assistant 🐭	Candela Medina	Buenos Aires (ARG)
Teaching Assistant 🖥️	Facundo Emina	Buenos Aires (ARG)	GitHub	@facuemina
Teaching Assistant 🖥️	Nirel Kadzo	Rwanda	GitHub	@Nirelkadzo
Teaching Assistant 🐀	Konrad Danielewski	🛰️ online	GitHub	@Nyktofob
Teaching Assistant 🐟	Virginia Palieri	🛰️ online	GitHub
Teaching Assistant 🔬	Aleksandra Gavrilova	Okinawa (JP)	GitHub	@shura_gav
Teaching Assistant 🖥️	Anastasiia Filippova	🛰️ online	GitHub	@NasFilippova
Teaching Assistant 🐟	Shuhong Huang	Munich (DE)	GitHub	@huang_shuhong
Teaching Assistant 🔬	Saffira Tjon	Okinawa (JP)	GitHub
Teaching Assistant 📸	Vic Shao-Chih Chiang	Toronoto (CA)	GitHub	@vsccvscc
Teaching Assistant 🐒	Rae Pineda	🛰️ online	GitHub	@rizaraep
Teaching Assistant 🐭	Anna Teruel-Sanchis	València (ESP)	GitHub	@annateruel_
Teaching Assistant 🖥️	Guillermo Hidalgo	Bochum (DE)	GitHub	@G_HidalgoGadea
Teaching Assistant 🖥️	Melanie Segado	🛰️ online	GitHub	@quietscientific
Teaching Assistant 🖥️	Niels Poulsen	Geneva (CH)	GitHub

Teaching Team for the first edition, anno 2022 🏆

Thanks to the whole teaching team for putting this together 🎉🎉🎉! Check out the Cajal course for the 2022 edition: Modern Methods for Quantifying Behavior

Role 🔥	Name 📛	Hub 🗺️📍	GitHub 🛠️	Twitter 🐥
Co - Director 🎖️	Alexander Mathis	🛰️ online	GitHub	@TrackingPlumes
Co - Director 🎖️	Danbee Kim	🛰️ online	GitHub	@taunbot
Cajal Administrator 📝	Elena Drosti	🛰️ online
Teaching Assistant 🦅	Sofia Minano	London (UK)	GitHub	@SofiMinano
Teaching Assistant 🐭	Nicole Vissers	London (UK)	GitHub	@NicoleVissers1
Teaching Assistant 🦇	Jonas Håkansson	Colorado Springs (USA)	GitHub	@ScientistJonas
Teaching Assistant 🐦	Neslihan Wittek	🛰️ online	GitHub	@taubenmaedel
Teaching Assistant 🐭	Andrada Marica	🛰️ online	GitHub	@andrada_marica
Teaching Assistant 🐭	Sabrina Benas	Buenos Aires (ARG)	GitHub	@Sabrineiitor
Teaching Assistant 🐤	Cecilia Herbert	Buenos Aires (ARG)	GitHub	@ChuckleScience
Teaching Assistant 🖥️	Facundo Emina	Buenos Aires (ARG)	GitHub	@facuemina
Teaching Assistant 🖥️	Nirel Kadzo	Nairobi (KEN)	GitHub	@Nirelkadzo
Teaching Assistant 🐭	Zane Mitrevica	🛰️ online	GitHub	@Zanemit
Teaching Assistant 🐀	Konrad Danielewski	Warsaw (PL)	GitHub	@Nyktofob
Teaching Assistant 🐟	Virginia Palieri	Munich (DE)	GitHub
Teaching Assistant 🖥️	Aleksandar Gavric	🛰️ online	GitHub	@AcaGavric
Teaching Assistant 🔬	Aleksandra Gavrilova	Okinawa (JP)	GitHub	@shura_gav
Teaching Assistant 🖥️	Anastasiia Filippova	🛰️ online	GitHub	@NasFilippova
Teaching Assistant 🐟	Shuhong Huang	Munich (DE)	GitHub	@huang_shuhong
Teaching Assistant 🔬	Saffira Tjon	Okinawa (JP)	GitHub

Acknowledgments

Naturally this material is partially based on DeepLabCut's Jupyter book as well as DeepLabCut in general. The same license applies.

See contributors for a list of individual contributors! In particular, thanks to the whole teaching team for putting this together.

This course received much support from the CAJAL Advance Neuroscience Training Programme. Have a look HERE and follow them @Cajal_Training for updates!

We are grateful for funding by the ChanZuckerberg Initiative: Essential Open Source Software for Science. Thanks!

dlc-cajal-course's Issues

Welcome teaching assistants!

We are looking forward to work with you!

Please check out the materials provided here. Ultimately, this will be a public Jupyter Book, just like the one of DeepLabCut!

For now, if you want to see it, you have to compile it locally with:

(first install): pip install -U jupyter-book
From the main folder, run the following command: jupyter-book build .
Then just open the index.html file in _build/html/index.html

To dos -- please help :)

There are quite a few TODO's in the document. They come in many flavors:

• TODO_TA are todos for all teaching assistants!
• TODO_AM are todos for me. You can help ;)
• more generally these personalized ones also exist for other people like Danbee... TODO_DK.

You can look for them by searching in GitHub, e.g. like this:

or of course in the cloned repository with any code editor.

Feedback?

Any other feedback is also welcome, please just open issues/PRs or discuss on discord or by email!

separate link under each steps, links should open in new tabs!

Discussion of datasets and your recommendations

Final updates

• link BUCTD video and mention DLC3
• update Modelzoo part -- GUI updates: DeepLabCut/DeepLabCut#2431
• update Cebra, #92
• final check

Feedback ideas based on your feedback just now :)

Thanks to all the feedback!

Already beforehand share:

• What minimal specs do you need for a computer if you want to use DLC (efficiently)?
• What limitations does COLAB have?
• Do you want to use the GUI / COLAB?
• already install DLC, read rel. papers
• share what you're interested in multi-animal / DLC live / ... / clustering / action segmentation / kinematics / neural data ..

Day 2 feedback:

• How to pick the most representative frames?
• What parameters are relevant for what?
• Can we train models for students over night (for students without GPU access)? --> mostly COLAB should be ideal?

Day 3 feedback:

• how to measure speed / benchmark runtime ?
• include further reading recommendations and refs in lecture page

Specific formatting feedback:

• #23
• one can link notebooks in a Jupyter book: https://jupyterbook.org/en/stable/content/executable/index.html --> (oner relevant notebook is: https://github.com/DeepLabCut/DeepLabCut/blob/master/examples/COLAB/COLAB_YOURDATA_TrainNetwork_VideoAnalysis.ipynb)
• also link to relevant time intervals of video tutorials for GUI

General problem solving:

• What have people struggled with? --> with solutions! (also link to the [DeepLabCut Forum(https://forum.image.sc/t/behavior-and-deeplabcut/23710) and Forum solutions). --> @KonradDanielewski
• Start FAQ section --> @KonradDanielewski
• Glossary of terms --> make section in resources @KonradDanielewski
• Link for prerequisites --> make section in resources @KonradDanielewski

Please add more aspects that I forgot?

Would be good to add behavior refs for day 1

-> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760923/
-> Krakauer et al. 2017