https://github.com/int-brain-lab/neuropixels_course_2024

Resources for the IBL portion of the UCL Neuropixels Course 2024
https://github.com/int-brain-lab/neuropixels_course_2024

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Resources for the IBL portion of the UCL Neuropixels Course 2024

• Host: GitHub
• URL: https://github.com/int-brain-lab/neuropixels_course_2024
• Owner: int-brain-lab
• License: mit
• Created: 2024-09-03T09:35:41.000Z (4 months ago)
• Default Branch: main
• Last Pushed: 2024-10-16T11:52:43.000Z (2 months ago)
• Last Synced: 2024-10-18T07:52:13.364Z (2 months ago)
• Language: Jupyter Notebook
• Size: 9.93 MB
• Stars: 7
• Watchers: 3
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Material for UCL Neuropixels Course 2024

This repository contains resources and assignments for the UCL Neuropixels Course 2024.

## Course Preparation

Prior to the course we recommend that you work through the installation and data download sections to ensure you have all the necessary software installed and have access to the data that 

will be used during the assignments:

- [Link to installation instructions for the IBL-related content](https://github.com/int-brain-lab/neuropixels_course_2024/tree/main/installation)

- [Link to data download instructions for the IBL-related content](https://github.com/int-brain-lab/neuropixels_course_2024/tree/main/data_access)

- [Link to preparation instructions for UnitMatch](https://github.com/int-brain-lab/neuropixels_course_2024/tree/main/UnitMatch#prerequisites)

- Link to installation instructions for [Bombcell](https://github.com/Julie-Fabre/bombcell). For now, bombcell is in MATLAB-only, but a Python version is coming in the next month. If you need a MATLAB license, see the details on slack or message us: [[email protected]](mailto:[email protected])

- Link to installation instructions for [phy](https://github.com/cortex-lab/phy?tab=readme-ov-file#installation-instructions)

- [Link to the Paxinos Atlas](https://drive.google.com/file/d/1aOHip11jth4LXYRG9qthwddmT1OxCOKX/view?usp=sharing)

If you run into any issues during the installation or data download process please write a message in the Neuropixels course dedicated slack channel or make an in [issue in this repository](https://github.com/int-brain-lab/neuropixels_course_2024/issues).

## Assignments

Please refer to the instructions in the individual folders for the following assignments.

**Day 1**

- [1.8.2 and 1.8.3 Practical: Spike sort raw data and inspect results with viewephys](viewephys/README.md)

**Day 2**

- 2.5.1 Practical: Quality control with Bombcell, Phy and IBL metrics:

  - [Bombcell + Phy](https://github.com/bombcell/Neuropixels_course_2024)

  - [IBL](https://github.com/int-brain-lab/neuropixels_course_2024/tree/main/quality_control_for_np_data)

- [2.5.2 Practical: Align data to histology](https://github.com/int-brain-lab/neuropixels_course_2024/tree/main/aligning_spikes_to_histology)

- [2.5.3 Practical: Analyze neural activity on the IBL website](https://github.com/int-brain-lab/neuropixels_course_2024/tree/main/functional_analysis)

- [2.5.4 Practical: Match neurons across days with UnitMatch](https://github.com/int-brain-lab/neuropixels_course_2024/tree/main/UnitMatch#assignment-match-neurons-across-days-with-unitmatch-254)

## Reference

[IBL spike sorting white paper](https://figshare.com/articles/online_resource/Spike_sorting_pipeline_for_the_International_Brain_Laboratory/19705522?file=35040628)