Update README.md

Author: r1chardrnn

ves_ncls/README.md

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+# Cluster Analysis of Vesicle Morphology
 
+## 1. Overview
+
+This project performs a cluster analysis on morphological data of vesicles to identify distinct structural groups. The analysis uses a dataset of 20 vesicle samples, characterized by a combination of numerical (e.g., 'TotalVol', 'NucVol', 'TotalLen') and categorical (e.g., 'Branch' type) features.
+
+The primary methods employed include:
+* Log transformation for numerical features.
+* Gower's distance to handle mixed data types.
+* Hierarchical agglomerative clustering (complete linkage method).
+* Cluster identification based on a distance threshold of 0.4.
+* Visualization of results using a dendrogram and a 2D Multidimensional Scaling (MDS) plot.
+
+This repository contains the Google Colab notebook used for the analysis.
+
+## 2. Relationship to Academic Paper
+
+This code and the accompanying notebook, `Cluster_Analysis_Morphology_Vesicle.ipynb`, are provided as supplementary material for the research paper:
+
+**[Your Paper Title Here - e.g., "Automated Morphological Classification of Vesicles using Hierarchical Clustering"]**
+
+*(Optional: Add authors, venue, or a link to the preprint/publication if available)*
+
+The notebook allows for the full reproduction of the clustering results and visualizations presented in the paper.
+
+## 3. File Structure
+
+* `README.md`: This file.
+* `Cluster_Analysis_Morphology_Vesicle.ipynb`: The Google Colab notebook containing all Python code, analysis steps, and embedded data.
+* *(Optional: Add here if you have separate data files, figure outputs, etc. e.g., `figures/dendrogram.png`)*
+
+## 4. Prerequisites and Dependencies
+
+The analysis is performed in a Python environment. The key dependencies are:
+* Python 3.x
+* pandas
+* numpy
+* scipy (for spatial distance, cluster hierarchy)
+* gower
+* matplotlib (for plotting)
+* scikit-learn (for MDS)
+
+The notebook includes a command to install the `gower` library:
+```bash
+!pip3 install gower