# Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks

## TL;DR

Uchimata is a toolkit that allows users to visualize 3D genome structures in web browsers and Jupyter Notebooks.

## Contribution

Uchimata introduces a flexible and integrable toolkit for 3D genome visualization combining JavaScript and Python.

## Key findings

- Uchimata provides a JavaScript library and Python widget for rendering 3D genome structures.
- The toolkit supports expressive visual encodings and filtering based on genomic and spatial criteria.
- Uchimata is open-source and integrates well with existing Python-based bioinformatics tools.

## Abstract

Uchimata is a toolkit for visualization of 3D structures of genomes. It consists of two packages: a Javascript library facilitating the rendering of 3D models of genomes, and a Python widget for visualization in Jupyter Notebooks. Main features include an expressive way to specify visual encodings, and filtering of 3D genome structures based on genomic semantics and spatial aspects. Uchimata is designed to be highly integratable with biological tooling available in Python.

Uchimata is released under the MIT License. The Javascript library is available on NPM, while the widget is available as a Python package hosted on PyPI. The source code for both is available publicly on Github (https://github.com/hms-dbmi/uchimata and https://github.com/hms-dbmi/uchimata-py) and Zenodo (https://doi.org/10.5281/zenodo.17831959 and https://doi.org/10.5281/zenodo.17832045). The documentation with examples is hosted at https://hms-dbmi.github.io/uchimata/.