From 832e4c0be978d83299e2cc356a80190a46c3379f Mon Sep 17 00:00:00 2001 From: Carsen Stringer Date: Fri, 18 Oct 2024 15:54:02 -0400 Subject: [PATCH] adding TOC to readme --- README.md | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/README.md b/README.md index 9d95865..e9f68b3 100644 --- a/README.md +++ b/README.md @@ -17,6 +17,28 @@ Rastermap is a discovery algorithm for neural data. The algorithm was written by Stringer C., Zhong L., Syeda A., Du F., Kesa M., & Pachitariu M. (2024). Rastermap: a discovery method for neural population recordings. *Nature Neuroscience*. https://doi.org/10.1038/s41593-024-01783-4. +Table of Contents +================= + +* [Rastermap](#rastermap) + * [Example notebooks](#example-notebooks) +* [Installation](#installation) + * [Local installation (< 2 minutes)](#local-installation--2-minutes) + * [System requirements](#system-requirements) + * [Instructions](#instructions) + * [Dependencies](#dependencies) +* [Using rastermap](#using-rastermap) + * [GUI](#gui) + * [In a notebook](#in-a-notebook) + * [From the command line](#from-the-command-line) + * [From MATLAB](#from-matlab) +* [Inputs](#inputs) +* [Settings](#settings) +* [Outputs](#outputs) +* [License](#license) + +### Example notebooks + Rastermap runs in python 3.8+ and has a graphical user interface (GUI) for running it easily. Rastermap can also be run in a jupyter notebook locally or on google colab, see these demos: * [rastermap_largescale.ipynb](notebooks/rastermap_largescale.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MouseLand/rastermap/blob/main/notebooks/rastermap_largescale.ipynb) shows how to use it with large-scale data from mouse cortex (> 200 neurons) * [rastermap_singleneurons.ipynb](notebooks/rastermap_singleneurons.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MouseLand/rastermap/blob/main/notebooks/rastermap_singleneurons.ipynb) shows how to use it with small to medium sized data (< 200 neurons), in this case recorded from rat hippocampus