From d8cbc9c61ae80c33dbca507f67083c372aa85810 Mon Sep 17 00:00:00 2001
From: Sharon Yates <30626642+sharoncy@users.noreply.github.com>
Date: Thu, 14 Mar 2024 10:39:28 +0100
Subject: [PATCH] Update README.md

---
 README.md | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index e46eb91..db52fa8 100644
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 # PyNutil
-PyNutil is a Python library for brain-wide quantification and spatial analysis of features in histological images from mouse and rat brain. It aims to replicate the Quantifier feature of the Nutil software (RRID: SCR_017183), to be intergrated with the other QUINT workflow web-tools. It builds on registration to a standardised reference atlas with the QuickNII (RRID:SCR_016854) and VisuAlign software (RRID:SCR_017978) and feature extraction by segmentation with an image analysis software such as ilastik (RRID:SCR_015246). 
+PyNutil is a Python library for brain-wide quantification and spatial analysis of features in serial section images from mouse and rat brain. It aims to replicate the Quantifier feature of the Nutil software (RRID: SCR_017183) to be run locally or to be intergrated with the QUINT workflow web-tools. It builds on registration to a standardised reference atlas with the QuickNII (RRID:SCR_016854) and VisuAlign software (RRID:SCR_017978) and feature extraction by segmentation with an image analysis software such as ilastik (RRID:SCR_015246). 
 
 For more information about the QUINT workflow:
 https://quint-workflow.readthedocs.io/en/latest/ 
+
+# Usage
+Run testOOP.py outside of the PyNutil directory.
+
+```
+from PyNutil import PyNutil
+
+pnt = PyNutil(settings_file=r"PyNutil/test/test.json")
+
+pnt.get_coordinates(object_cutoff=0, use_flat=False)
+
+pnt.quantify_coordinates()
+
+pnt.save_analysis("PyNutil/outputs/myResults")
+```
  
 # Acknowledgements
 PyNutil is developed at the Neural Systems Laboratory at the Institute of Basic Medical Sciences, University of Oslo, Norway with support from the EBRAINS infrastructure, and funding support from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA).
-- 
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