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Feature Explorer

Feature Explorer is a Python dashboard application for exploring OME-Zarr images alongside tabular data, specifically designed to work with outputs from the Fractal Image Analysis platform.

Overview

Feature Explorer provides an interactive web-based interface for visualizing and analyzing multi-dimensional image datasets with associated quantitative measurements and metadata.

Environment

Environment: feature-explorer

Available Tasks

Start Feature Explorer Dashboard

Launch the interactive Feature Explorer dashboard:

pixi run feature-explorer

Features

  • Interactive visualization: Web-based dashboard for image and data exploration
  • OME-Zarr support: Native support for OME-Zarr image format
  • Tabular data integration: Seamlessly combine images with measurement data
  • Multi-dimensional navigation: Explore 2D, 3D, and time-series datasets
  • Feature analysis: Visualize and analyze extracted quantitative features
  • Fractal integration: Optimized for Fractal Image Analysis platform outputs
  • Real-time filtering: Interactive filtering and selection of data points
  • Export capabilities: Export visualizations and filtered datasets

Supported Data Types

Image Data

  • OME-Zarr format: Multi-resolution, chunked image arrays
  • Multi-channel images: Fluorescence microscopy with multiple markers
  • Time-series data: Time-lapse imaging datasets
  • 3D volumes: Confocal and light-sheet microscopy data

Tabular Data

  • Feature measurements: Quantitative measurements extracted from images
  • Metadata: Experimental conditions and sample information
  • Segmentation results: Object properties and classifications
  • Statistical summaries: Aggregated measurements and statistics

Dashboard Components

Image Viewer

  • Multi-dimensional image display with zoom and pan
  • Channel selection and blending
  • Overlay of segmentation masks and annotations
  • Real-time image updates based on data selection

Data Explorer

  • Interactive tables with sorting and filtering
  • Statistical plots and histograms
  • Correlation analysis and scatter plots
  • Feature distribution visualization

Analysis Tools

  • Quality control metrics and visualizations
  • Batch comparison tools
  • Export functionality for further analysis
  • Integration with downstream analysis pipelines

Getting Started

  1. Make sure you have pixi installed and this repository cloned
  2. Navigate to the repository directory
  3. Run pixi run feature-explorer to start the dashboard
  4. Open your browser and navigate to the provided URL
  5. Load your OME-Zarr images and associated tabular data
  6. Start exploring your datasets interactively!

Use Cases

  • Quality control: Assess image quality and analysis results
  • Data exploration: Discover patterns and relationships in large datasets
  • Result validation: Validate automated analysis results
  • Comparative analysis: Compare results across different experimental conditions
  • Visualization: Create publication-ready figures and visualizations
  • Data filtering: Select subsets of data for downstream analysis

Integration with Fractal

Feature Explorer is specifically designed to work with outputs from the Fractal Image Analysis platform, providing: - Direct loading of Fractal workflow outputs - Visualization of processing results at each workflow step - Quality assessment of automated analysis pipelines - Interactive exploration of large-scale analysis results

Resources