diff --git a/README.md b/README.md
index 4c4e84c7f41cce392c2d1b09439c451d9c8ab963..2e8c40adc25e114f9767e067e3db0e8586287589 100644
--- a/README.md
+++ b/README.md
@@ -11,11 +11,12 @@ End-to-end processing of cell microscopy time-lapses. ALIBY automates segmentati
 ## Quickstart Documentation
 Installation of [VS Studio](https://visualstudio.microsoft.com/downloads/#microsoft-visual-c-redistributable-for-visual-studio-2022) Native MacOS support for is under work, but you can use containers (e.g., Docker, Podman) in the meantime.
 
-For analysing local data
+To analyse local data
  ```bash
-pip install aliby # aliby[network] if you want to access an OMERO server
+pip install aliby 
  ```
-
+ Add any of the optional flags `omero` and `utils` (e.g., `pip install aliby[omero, utils]`). `omero` provides tools to connect with an OMERO server and `utils` provides visualisation, user interface and additional deep learning tools.
+  
 See our [installation instructions]( https://aliby.readthedocs.io/en/latest/INSTALL.html ) for more details.
 
 ### CLI
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 6d3af3b594b0af2f4581c0a5d0221abe85b1cdca..d415b3f3c53b46658b4ce26258302beed00972a4 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -4,7 +4,6 @@
    contain the root `toctree` directive.
 
 .. toctree::
-   :hidden:
 
    Home page <self>
    Installation <INSTALL.md>
diff --git a/src/aliby/bin/__init__.py b/src/aliby/bin/__init__.py
index a051bb08ab05961eccb8250a04ca9bf4f0e382d9..916e95289f298cdba6003d680867e73d05b8e0d4 100644
--- a/src/aliby/bin/__init__.py
+++ b/src/aliby/bin/__init__.py
@@ -1 +1,3 @@
-#!/usr/bin/env jupyter
+"""
+Command Line Interface utilities.
+"""
diff --git a/src/aliby/lineage/__init__.py b/src/aliby/lineage/__init__.py
index a051bb08ab05961eccb8250a04ca9bf4f0e382d9..7105ba3529ec3ee49065968271c5c5ea2c830e2d 100644
--- a/src/aliby/lineage/__init__.py
+++ b/src/aliby/lineage/__init__.py
@@ -1 +1,3 @@
-#!/usr/bin/env jupyter
+"""
+Models that link regions of interest, such as mothers and buds.
+"""
diff --git a/src/aliby/lineage/bud_tracker.py b/src/aliby/lineage/bud_tracker.py
index ef6a2e46820e15908dc92dc31a3eec9d398b1a14..659e690dd1d84b8533dadb42d4aa1c629e864297 100644
--- a/src/aliby/lineage/bud_tracker.py
+++ b/src/aliby/lineage/bud_tracker.py
@@ -1,4 +1,8 @@
-#!/usr/bin/env jupyter
+"""
+Extracted from the baby repository. Bud Tracker algorithm to link
+cell outlines as mothers and buds.
+"""
+# /usr/bin/env jupyter
 
 import pickle
 from os.path import join
diff --git a/src/postprocessor/core/lineageprocess.py b/src/postprocessor/core/lineageprocess.py
index 856d079130d3d61486c1a36d4f7146991afc0322..8c2874e24c48e81257612b0c536b27e299070a5a 100644
--- a/src/postprocessor/core/lineageprocess.py
+++ b/src/postprocessor/core/lineageprocess.py
@@ -21,7 +21,7 @@ class LineageProcessParameters(ParametersABC):
 
 class LineageProcess(PostProcessABC):
     """
-    Lineage process that must be passed a (N,3) lineage matrix (where the coliumns are trap, mother, daughter respectively)
+    Lineage process that must be passed a (N,3) lineage matrix (where the columns are trap, mother, daughter respectively)
     """
 
     def __init__(self, parameters: LineageProcessParameters):