From 23177c239219ae4f02a27d67917cd9d198b05748 Mon Sep 17 00:00:00 2001
From: Joe Ziminski <55797454+JoeZiminski@users.noreply.github.com>
Date: Fri, 7 Feb 2025 17:33:03 +0000
Subject: [PATCH] Update README.md

---
 README.md | 68 +++++++++++++++++++++++++++++++++++++++++++++++++++----
 1 file changed, 63 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index cc5e955..4e98ea0 100644
--- a/README.md
+++ b/README.md
@@ -2,12 +2,70 @@
 
 ``spikewrap`` is a tool for automating extracellular electrophysiology analysis.
 
-See the documentation to a 
-[1-minute introduction](https://spikewrap.neuroinformatics.dev/gallery_builds/get_started/package_overview.html)
-and to 
-[get started](https://spikewrap.neuroinformatics.dev/get_started/index.html).
+See the documentation for a quick
+[feature overview](https://spikewrap.neuroinformatics.dev/gallery_builds/get_started/feature_overview.html)
+and to [get started](https://spikewrap.neuroinformatics.dev/get_started/index.html).
 
+## Overview
+
+``spikewrap`` provides a lightweight interface to manage the preprocessing and sorting 
+of extracellular electrophysiological data. 
+
+Built on [SpikeInterface](https://spikeinterface.readthedocs.io/en/stable/api.html), ``spikewrap`` offers a convenient wrapper
+to run sorting pipelines. It aims to facilitate the sharing of electrophysiology pipelines and standardize project folders.
+
+For example, all runs for a recording session can be preprocessed with:
+
+```
+import spikewrap as sw
+
+subject_path = sw.get_example_data_path() / "rawdata" / "sub-001"
+
+session = sw.Session(
+    subject_path=subject_path,
+    session_name="ses-001",
+    file_format="spikeglx",  # or "openephys"
+    run_names="all",
+    probe=None,  # optional argument to set probe (neuropixels auto-detected)
+)
+
+session.preprocess(
+    configs="neuropixels+kilosort2_5",
+    per_shank=True,
+    concat_runs=True,
+)
+
+session.save_preprocessed(
+    overwrite=True,
+    n_jobs=12,
+    slurm=True
+)
+```
+
+This will output a folder structure like:
+
+```
+└── derivatives/
+    └── sub-001/
+        └── ses-001  /
+            └── ephys/
+                └── concat_run/
+                    ├── preprocessed/
+                    │   ├── shank_0/
+                    │   │   └── si_recording/
+                    │   │       └── <spikeinterface binary>
+                    │   └── shank_1/
+                    │       └── si_recording/
+                    │           └── <spikeinterface binary> 
+                    └── sync/
+                    │   └── sync_channel.npy
+                    └── orig_run_names.txt
+```                   
 
 ## Installation
 
-``pip install spikewrap``
+``pip install spikewrap`` 
+
+## Get Involved
+
+Contributions to ``spikewrap`` are welcome and appreciated! Please see our [contributing guide](https://spikewrap.neuroinformatics.dev/community/contributing_guide.html) for details, and don't hesitate to ask any questions on our [Zulip Chat](https://neuroinformatics.zulipchat.com/#narrow/stream/406002-Spikewrap).