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🛠️ Installation Guide

This guide covers how to set up the Bacterial Generation Determination pipeline. You can choose to run the analysis in the cloud (Google Colab) or on your local machine.

🚀 Option 1: Google Colab (Zero Setup)

Recommended for most users.

You do not need to install Python or any libraries. The notebook handles the environment setup automatically.

  1. Open the Notebook: Click the "Open in Colab" badge in the main README or click here.

  2. Run the Setup Cell: The very first code cell in the notebook contains a script that detects you are in Colab and runs:

    !pip install -q pandas numpy matplotlib seaborn scipy networkx

Connect Data: The notebook will ask you to mount Google Drive. Ensure your TrackMate .csv files are uploaded to your Drive before starting.

💻 Option 2: Local Computer Best for heavy processing or users who prefer privacy/offline access.

Prerequisites Python 3.8 or higher.

Git (to download the repository).

A terminal (Command Prompt, PowerShell, or Terminal).

Step-by-Step Installation

  1. Download the Repository Open your terminal and run:

bash git clone https://github.com/JoeVPhD/TrackMate_CellPose_Bacterial_Generation_Determination.git cd TrackMate_CellPose_Bacterial_Generation_Determination (Alternatively, you can download the ZIP file from GitHub and unzip it.)

  1. Set Up a Virtual Environment (Recommended) It is best practice to isolate this project so it doesn't conflict with other Python tools you use.

Using Conda (Anaconda/Miniconda):

bash conda create -n bacterial_tracker python=3.10 conda activate bacterial_tracker Using Standard Python (venv): Windows:

bash python -m venv venv .\venv\Scripts\activate Mac/Linux:

bash python3 -m venv venv source venv/bin/activate 3. Install Dependencies We provide a requirements.txt file that lists all necessary libraries (Pandas, NetworkX, SciPy, etc.).

bash pip install -r requirements.txt 4. Launch Jupyter Start the notebook interface:

bash jupyter notebook TrackMate_CellPose_Bacterial_Generation_Determination.ipynb ⚠️ Troubleshooting "ModuleNotFoundError: No module named..."

You likely forgot to run pip install -r requirements.txt.

If you are in Conda, make sure you ran conda activate bacterial_tracker first.

"FileNotFoundError" when loading data

Ensure your input files follow the naming convention:

ExperimentName_spots.csv

ExperimentName_edges.csv

Windows Users: Avoid spaces in your folder paths if possible.

Graphviz / NetworkX Errors

This pipeline uses networkx which is pure Python. You generally do not need to install system-level Graphviz binaries for this specific notebook.

text

Update your main README.md

Now, in your main README, simply add a clear, short pointer to this new file.

Add this to README.md:

## 📦 Installation
For detailed instructions on setting up this tool locally or on Google Colab, please see our [Installation Guide](INSTALLATION.md).

**Quick Start:**
- **Cloud:** Click the "Open in Colab" badge above.
- **Local:** `pip install -r requirements.txt`