Flatiron CCN Software Workshop, February 2025

We are excited to see everyone at the Flatiron Center for Computational Neuroscience workshop on using open source packages to analyze neural data in February 2025!

Over the course of this two-day workshop, we will walk you through the notebooks included on this site in order to demonstrate how to use pynapple and NeMoS to analyze and visualize your data.

This website contains links to the presentations for the workshop, as well as to other useful information.

Useful links

Workshop schedule
Notebook site
Websites for the packages used in this workshop:
- pynapple: documentation, github repo, twitter, bluesky
- NeMoS: documentation, github repo, twitter

Setup

Before the workshop begins, please follow the setup instructions found on the workshop notebook site

Presentations, in chronological order

Intro to CCN, Eero Simoncelli
Welcome, Billy Broderick (pdf version)
Neurodata Without Borders, Oliver Rübel
Pynapple, Guillaume Viejo
Signal processing and decoding, Sarah Jo Venditto
fastplotlib, Kushal Kolar
A conceptual introduction to Generalized Linear Models, Edoardo Balzani
Basic Generalized Linear Models with NeMoS, Billy Broderick (pdf version)
Model Selection and Cross-Validation, Edoardo Balzani
scikit-learn and nemos, Billy Broderick (pdf version)
Conclusion, Billy Broderick (pdf version)

Schedule

Day 0 (Tues, Feb 4)
1pm – 2pm	Welcome and networking lunch
2pm – 5pm	Installation help
Day 1 (Wed, Feb 5)	pynapple
10 – 11am	Welcome and introduction to data standards
11 – 11:30am	Coffee break
11:30am – 1pm	Pynapple core
1 – 2pm	Lunch
2 – 3:30pm	Standard analyses in systems neuroscience, part 1: cross-correlations and tuning curves
3:30 – 4pm	Participant photo and Coffee break
4 – 5:45pm	Standard analyses in systems neuroscience, part 2: signal processing
5:45 – 6pm	fastplotlib advertisement
Day 2 (Thurs, Feb 6)	NeMoS
10 – 11am	Introduction to Generalized Linear Models (GLMs)
11 – 11:30am	Coffee break
11:30am – 1pm	Fitting a basic GLM to single neuron patch-clamp recordings
1 – 2pm	Lunch
2 – 4pm	Functional connectivity analysis of head-direction neurons
4 – 4:30pm	Coffee break
4:30 – 6pm	Feature selection and model comparison
6 – 8pm	Concluding reception