Revision 4dd1adddad54627601f7567354fa7f0af020fc7d authored by Guillaume Viejo on 05 July 2023, 20:05:21 UTC, committed by GitHub on 05 July 2023, 20:05:21 UTC
update link to pynapple documentation
README.md
# pynacollada 🍍 🥥 🍹
Collaborative platform for high-level analysis with pynapple.
- [pynacollada](#pynacollada)
* [Getting Started](#getting-started)
+ [Requirements](#requirements)
+ [Installation](#installation)
* [Libraries](#libraries)
+ [Neural Ensembles](#neural-ensembles)
+ [Manifolds](#manifolds)
+ [EEG processing](#eeg-processing)
+ [PETH](#peth)
+ [Brain state scoring](#brain-state-scoring)
+ [Graphics](#graphics)
+ [Position tracking](#position-tracking)
> **Note**
> See the analysis of the pynapple paper [here](https://github.com/PeyracheLab/pynacollada/tree/main/pynacollada/Pynapple%20Paper%20Figures)
## Getting Started
### Requirements
- Python 3.6+
- [pynapple](https://github.com/PeyracheLab/pynapple)
- scikit-learn
- seaborn
### Installation
<!-- pynacco can be installed with pip:
``` {.sourceCode .shell}
$ pip install pynapple==0.2.0a1
```
-->
Directly from the source code:
``` {.sourceCode .shell}
$ # clone the repository
$ git clone https://github.com/PeyracheLab/pynacollada.git
$ cd pynacollada
$ # Install in editable mode with `-e` or, equivalently, `--editable`
$ pip install -e .
```
## Libraries
| | **Jupyter notebook / scripts** | **Description** | **Contributors** |
|-------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------|------------------|
| **_Neural Ensembles_** | [Neuralensemble_tutorial_replay1.ipynb](pynacollada/neural_ensemble/Neuralensemble_tutorial_replay1.ipynb) <br/> [pynacollada_tutorial_replay_short.py](pynacollada/neural_ensemble/pynacollada_tutorial_replay_short.py) | How to use pynapple to compute sleep reactivation, step by step. | Adrien Peyrache |
| **_Manifolds_** | [Tutorial_manifold_ring.ipynb](pynacollada/neural_manifold/Tutorial_manifold_ring.ipynb) | How to project a ring manifold with head-direction neurons. | Guillaume Viejo |
| **_EEG processing_** | [Tutorial_ripple_detection.ipynb](pynacollada/eeg_processing/Tutorial_ripple_detection.ipynb) <br/> [Tutorial_ripple_detection.py](pynacollada/eeg_processing/Tutorial_ripple_detection.ipynb) | How to detect ripples in CA1 step by steps. | Guillaume Viejo |
| **_PETH_** | [Tutorial_PETH_Ripples.ipynb](pynacollada/PETH/Tutorial_PETH_Ripples.ipynb) | How to make a peri-event time histogramm and raster plots around ripples. | Guillaume Viejo |
| **_Position tracking_** | [Tutorial_DeepLabCut_Path_Segmentation.ipynb](pynacollada/position_tracking/DLC_process_position.ipynb) | How to segment the path of a mouse running in a radial-arm maze with position extracted with DeepLabCut. | Dhruv Mehrotra |
| **_Waveform processing_** | [load_mean_waveforms.ipynb](pynacollada/waveform_processing/load_mean_waveforms.ipynb) | How to extract the mean waveforms from a binary file. | Sofia Skromne Carrasco |
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