Paper examples

This page provides examples of papers that have used MuSpAn in their research from our developers and community.

Tip

If you would like us to showcase notebook examples of your MuSpAn related publications, email us at info@muspan.co.uk with:

1. a link to the publication,

2. a brief summary (200 words max),

3. Python notebook tutorial(s) reproducing the results of the paper.

This increases the visibility of your work and helps others to understand how MuSpAn can be used in research.

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2024

MuSpAn: A Toolbox for Multiscale Spatial Analysis

Authors:	Joshua A. Bull, Joshua W. Moore, Eoghan J. Mulholland, Simon J. Leedham and Helen M. Byrne
Journal:	BioRxiv
Year:	2024
DOI:	https://doi.org/10.1101/2024.12.06.627195
Summary:	This paper presents MuSpAn, a versatile toolbox for multiscale spatial analysis. Designed as a flexible and extensible framework, MuSpAn offers a suite of statistical methods for analysing spatial data, including point pattern analysis, spatial networks, and topological data analysis. The paper demonstrates the toolbox’s multiscale capabilities using spatial transcriptomics data, showcasing its potential for diverse spatial analysis applications. These examples were made with MuSpAn v1.0.0.

MuSpAn: Figure 2. Quantification at the cell scale

MuSpAn: Figure 3. Quantification of cell-cell proximity

MuSpAn: Figure 4. Quantification of intercellular relationships across length scales

MuSpAn: Figure 5. Quantification of tissue scale features

MuSpAn: Figure 6. Biologically-driven pipeline development using MuSpAn

Integrating Diverse Statistical Methods to Analyse Stage-Discriminatory Cell Interactions in Colorectal Neoplasia

Authors:	Joshua A. Bull, Eoghan J. Mulholland, Joshua W. Moore, Jesús J. Bosque, Bernadette J. Stolz, Joseph Boen, Holly R. Eggington, Hayley L. Belnoue-Davis, Helen Jones, Chandler D. Gatenbee, Alexander R. A. Anderson, Alistair Easton, Peter Todd, Christopher Cunningham, Stephen Taylor, Helen M. Byrne and Simon J. Leedham
Journal:	BioRxiv
Year:	2024
DOI:	https://doi.org/10.1101/2024.06.02.597010
Summary:	In this study, MuSpAn is used to integrate a range of mathematical tools into a suite of spatial descriptors. These descriptors were deployed and integrated with interpretable ML to study how cell interactions evolve as colorectal cancer progresses from benign precursors to malignant states, demonstrating how combining diverse mathematical analyses can uncover insights into tissue organisation and identify the variable cell-cell relationships underlying disease progression. These examples were made with MuSpAn v1.0.0.

Analysing Cell-Cell Interactions in Colorectal Neoplasia: Figure 1.

More tutorials coming soon!

Extended correlation functions for spatial analysis of multiplex imaging data

Authors:	Joshua A. Bull, Eoghan J. Mulholland, Simon J. Leedham and Helen M. Byrne
Journal:	Biological Imaging
Year:	2024
DOI:	https://doi.org/10.1017/S2633903X24000011
Summary:	This paper introduces three extensions to the pair correlation function (PCF) to overcome its limitations, enabling more nuanced analysis of cell clustering, colocalisation, and spatial correlations in biological datasets.

Tutorials coming soon!