ndxplorer

ndXplorer is an interactive tool for analyzing and visualizing multidimensional data sets. It provides a user-friendly graphical interface for data exploration, dimensionality reduction, clustering, and visualization.

Overview

ndXplorer is designed to handle various types of multidimensional data, including:

• Multi-dimensional fluorescence (MFD) data
• Sampling of posterior distributions from ChiSurf
• Inter-label distance distributions from Olga
• General multidimensional scientific data

ndxplorer can be used as a standalone application or integrated into other software as a tool.

Features

• Interactive Data Visualization: Create and customize various plot types for multidimensional data
• Dimensionality Reduction: Apply UMAP (Uniform Manifold Approximation and Projection) for visualizing high-dimensional data
• Clustering Analysis: Perform clustering using algorithms like HDBSCAN and K-means
• Data Import/Export: Read and write data in various formats
• Curve Overlay: Overlay curves on plots for comparison
• Parameter Editing: Interactive editing of visualization parameters
• Code Editing: Built-in code editor for customization
• Customizable UI: Flexible user interface with theme support

Dependencies

ndXplorer requires the following dependencies:

• Python
• PyQt and QtPy (for GUI)
• NumPy, pandas, scipy (for data handling and computation)
• matplotlib and PyQtGraph (for plotting)
• UMAP-learn (for dimensionality reduction)
• HDBSCAN and scikit-learn (for clustering)
• guidata and guiqwt (for GUI components)

Installation

Using conda (recommended)

The easiest way to install ndXplorer is via conda:

conda install -c tpeulen ndxplorer

From source

To install from source:

git clone https://github.com/fluorescence-tools/ndxplorer.git
cd ndxplorer
pip install -e .

Usage

Starting ndXplorer

To start ndXplorer, simply run:

ndxplorer

Basic Workflow

1. Load Data: Import your multidimensional data
2. Explore: Use the interactive plots to explore your data
3. Analyze: Apply dimensionality reduction and clustering techniques
4. Visualize: Create custom visualizations of your data
5. Export: Save your results and visualizations

Contributing

Contributions to ndXplorer are welcome! Please feel free to submit a Pull Request.

License

ndXplorer is licensed under the GPL 2.1 License. See the LICENSE file for details.