fusion-tools

Modular creation of dashboards for visualization and analysis of histology data

What is fusion-tools?

fusion-tools was designed as a flexible way for users to generate interactive components which focus on histological images. It was designed in tandem with FUSION (Functional Units State Identification in WSIs), which focused on paired analysis of spatial –omics data. fusion-tools provides an easy-to-use (hopefully) interface for users to instantiate their own versions of FUSION with incorporation of locally stored data, develop their own interactive components, and design their own upload templates for new varieties of spatial data or new cloud-hosted plugins.

Installation

fusion-tools is deployed through PyPI and can be installed using:

`bash $ pip install fusion-tools `

If you would like to install a version of fusion-tools earler than v3.6.18 (July 2025) (Dash < 3.0.0, other minor changes), install with the following syntax:

`bash $ pip install fusion-tools[interactive]<=3.6.18 `

The “interactive” tag is necessary for accessing interactive component dependencies in early deployments.

large-image setup

fusion-tools uses large-image for all whole slide image (WSI) reading operations. The large-image library includes an extensive collection of different image file readers, however, due to some hardware/operating system requirements, fusion-tools includes only the following:

• openjpeg

• openslide

• tifffile

For a full list of image formats supported by large-image and installation instructions for each (or all), see [large-image documentation](https://girder.github.io/large_image/formats.html).

Table of contents

• Background
  • How did fusion-tools start?
  • What makes fusion-tools different from __________?
  • Where should I start?
• Introduction to Dash
  • Dash
• Digital Slide Archive (DSA)
  • fusion_tools.handler module
  • Digital Slide Archive (DSA) Integrated Components
• Visualization class
  • fusion_tools.visualization package
  • The Visualization Session
  • fusion_tools.visualization module
• Components Overview
  • Map Components
  • Plotting Components
  • Human Reference Atlas Components
  • Annotation Components
  • Download Components
  • Designing Custom Components
• Non-Interactive Functions and Utilities
  • Shape Utilities
  • Image Utilities
  • Omics Utilities

Citation

If you find this work useful in your own research, please consider citing:

Border, S.P., Ferreira, R.M., Lucarelli, N. et al. FUSION: a web-based application for in-depth exploration of multi-omics data with brightfield histology. Nat Commun 16, 8388 (2025). https://doi.org/10.1038/s41467-025-63050-9

``` @article{border2025fusion,

title={FUSION: A web-based application for in-depth exploration of multi-omics data with brightfield histology}, author={Border, Samuel P and Ferreira, Ricardo Melo and Lucarelli, Nicholas and Kumar, Suhas Katari Chaluva and Paul, Anindya S and Manthey, David and Barisoni, Laura and Levites Strekalova, Yulia A and Ray, Jessica and Cheng, Ying-Hua and others}, journal={Nature Communications}, volume={16}, number={1}, pages={8388}, year={2025}, publisher={Nature Publishing Group UK London}

}