docs(index): Include pipeline in index

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

docs/source/index.rst

@@ -4,7 +4,6 @@
    contain the root `toctree` directive.
 
 .. toctree::
-   :hidden:
 
    Home page <self>
    Installation <INSTALL.md>

src/aliby/bin/__init__.py

-#!/usr/bin/env jupyter
+"""
+Command Line Interface utilities.
+"""

src/aliby/lineage/__init__.py

-#!/usr/bin/env jupyter
+"""
+Models that link regions of interest, such as mothers and buds.
+"""

src/aliby/lineage/bud_tracker.py

-#!/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

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):