Flatiron CCN Software Workshop at SfN 2025

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

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

This website will contain links to the presentations for the workshop, as well as to other useful information. Check back soon! In the meantime, see our main page for previous workshop schedules and materials.

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

Welcome, Billy Broderick (pdf version)
Neurodata Without Borders, Heberto Mayorquin
Pynapple, Guillaume Viejo
A conceptual introduction to Generalized Linear Models, Edoardo Balzani
Basic Generalized Linear Models with NeMoS, Billy Broderick (pdf version)
Group project structure, Billy Broderick (pdf version)
Plenoptic, Billy Broderick (pdf version)
Advanced Pynapple, Sarah Jo Venditto
Signal processing and decoding, Sarah Jo Venditto
Model Selection and Cross-Validation, Edoardo Balzani
scikit-learn and nemos, Billy Broderick (pdf version)
Openscope Dataset, Camila Maura
Conclusion, Billy Broderick (pdf version)

Schedule

Day 0 (Wed, Nov 12)
12pm – 6pm	Installation help
4:30pm – 5:30pm	Jupyter Lab introduction
6pm – 8pm	Welcome reception
Day 1 (Thurs, Nov 13)	Day 1
9 – 10am	Breakfast
10 – 10:30am	Welcome
10:30 – 11am	Introduction to data standards
11 – 11:30am	Coffee break
11:30am – 1pm	Pynapple core
1 – 2pm	Lunch
2 – 4pm	NeMoS core
4 – 4:30pm	Coffee break
4:30 – 6pm	Group project: Analyzing head-direction population with Pynapple & Nemos
6 – 8pm	Dinner at hotel
Day 2 (Fri, Nov 14)	Day 2
9 – 10am	Breakfast
10 – 10:30am	Plenoptic advertisement
10:30 – 11am	Pynapple advanced
11 – 11:30am	Coffee break
11:30am – 1pm	Group project: Analyzing hippocampal place cells with Pynapple and NeMoS
1 – 2pm	Lunch
2 – 3:30pm	NeMoS advanced
3:30 – 4pm	Coffee break
4 – 6pm	Group project: Exploring the Allen Institute’s Visual Coding dataset
6:30 – 8pm	Dinner at Puesto (789 West Harbor Drive)