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Reposted by Josh Moore

Joshua Bull @joshuabull.bsky.social · 24/09/2026

MuSpAn will be at #ESSB2026! Both @josh-moore.bsky.social and I are discussing new mathematical methods that are making their way into the package, during the Computational #SpatialBiology session flash talks on Tuesday - or come and find us with any questions! Paper: doi.org/10.1038/s414...

doi.org

MuSpAn: a toolbox for multiscale spatial analysis - Nature Communications

Bull, Moore, and colleagues present MuSpAn, a flexible platform for analysing spatial biology data across scales. It integrates diverse methods to enable quantitative characterisation of tissue organi...

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Josh Moore @josh-moore.bsky.social · 13/07/2026

Straight-line distance isn't always the right way to measure spatial associations in biology. Introducing netPCF, geometry-aware pair correlation functions that estimate over the intrinsic geometry of biological spatial data. Available now in SpaceNet (and soon MuSpAn 👀) 📄 Paper: lnkd.in/eFmckM-J

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Josh Moore @josh-moore.bsky.social · 24/03/2026

We’ve just published a new paper using MuSpAn looking at how TGFβ perturbation reshapes immune–fibroblast interactions in tissue. Another example of therapeutic response being driven not just by composition, but by spatial reorganisation. Link below 🔗 www.cell.com/iscience/ful... 🧪🧬🔬💻

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Josh Moore @josh-moore.bsky.social · 23/03/2026

Earlier this month we ran the NMGN MuSpAn Hackathon in York, an intense, collaborative week bringing together maths & biology to tackle spatial transcriptomics with MuSpAn. Amazing energy, rapid insights, and some very exciting work already taking shape. Papers to follow… watch this space 👀

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Reposted by Josh Moore

Joshua Bull @joshuabull.bsky.social · 22/01/2026

Hi everyone, MuSpAn v1.2.2 is now available! Featuring lots of nice quality of life updates behind the scenes. Enjoy! docs.muspan.co.uk/latest/tutor... #spatialbiology #spatial #biology 🧬🧪👨‍🔬

docs.muspan.co.uk

Tutorials — Multiscale Spatial Analysis

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Reposted by Josh Moore

Joshua Bull @joshuabull.bsky.social · 16/10/2025

If you're at #ESSB2025 and are curious about alternative existing tools with the capacity to combine cell networks into larger objects for further analysis, and much much more, please come and talk to me about #MuSpAn at poster 58 this afternoon

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Josh Moore @josh-moore.bsky.social · 14/10/2025

Looking forward to a busy week of spatial biology at EMBL. If you’re at #ESSB2025 and interested spatial analysis and/or its use for identifying drug response, come find me at p151 (helix b)

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Reposted by Josh Moore

Joshua Bull @joshuabull.bsky.social · 25/09/2025

Our new MuSpAn preprint is now live, featuring additional examples and with expanded supplementary information: doi.org/10.1101/2024... This accompanies the release today of v1.2.0 of MuSpAn with new features, optimisations, and bug fixes: docs.muspan.co.uk/latest/Insta... 🧪🧬🖥️ #SpatialBiology

doi.org

MuSpAn: A Toolbox for Multiscale Spatial Analysis

Advances in multiplex imaging and spatial omics have revolutionised spatial data generation in biology, revealing complex tissue organisation across multiple scales. However, methods for analysing the...

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Josh Moore @josh-moore.bsky.social · 25/08/2025

Come work with us! We're hiring for roles in spatial data analysis and mathematical modelling @ Oxford, studying drug response and metastasis in colorectal cancer as part of the CRC-STARS programme. Spatial Data Analysis: lnkd.in/eMWEdQJt Modelling: lnkd.in/e5KVb-FT Deadline: 11/09/25

lnkd.in

This link will take you to a page that’s not on LinkedIn

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Reposted by Josh Moore

Joshua Bull @joshuabull.bsky.social · 17/07/2025

I couldn't make it to #SMB2025 this year, but my sources tell me #MuSpAn managed to make the journey over to Canada! If you enjoyed Sergio's talk, do take a look at docs.muspan.co.uk and see if it'd be useful for your data / agent based models / anything else spatial that you've got lying around!

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Reposted by Josh Moore

Joshua Bull @joshuabull.bsky.social · 27/05/2025

...and don't forget that the great @josh-moore.bsky.social is on site, if anyone wants to go and find him at Poster 23! #BICC2025 (Bring drinks, snacks, or other bribery, and he'll definitely be happy to help chat about your spatial biology needs!)

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Reposted by Josh Moore

Joshua Bull @joshuabull.bsky.social · 01/05/2025

In addition to the two #SpatialBiology posts in the thread below, we're now also advertising for a Research Software Engineer #RSE to help us take #MuSpAn to the next level - come and join us! my.corehr.com/pls/uoxrecru... #academic #jobs #softwaredeveloper #compsci

my.corehr.com

Job Details

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Reposted by Josh Moore

Joshua Bull @joshuabull.bsky.social · 14/03/2025

The cover art for this week's "This Week in Math Onco" newsletter has come straight out of MuSpAn! thisweekmathonco.substack.com/p/this-week-... Preprint here: doi.org/10.1101/2024...

thisweekmathonco.substack.com

This week in MathOnco 324

CAR-T, circulating tumor DNA, EMT transitions, ecological and evolutionary models...

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Josh Moore @josh-moore.bsky.social · 06/03/2025

Want to get more out of your spatial data? 🧪🔬 Check out MuSpAn with our latest release that brings new features, optimisation, more tutorials, a streamlined distribution and bug fixes! Find out more at docs.muspan.co.uk/latest/relea...

docs.muspan.co.uk

Release notes — Multiscale Spatial Analysis

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Reposted by Josh Moore

Joshua Bull @joshuabull.bsky.social · 09/01/2025

FYI for anyone interested in MuSpAn - we've updated the preprint this week with the full SI. Now featuring more examples of how various different spatial metrics can be strung together in order to make spatial pipelines focussed on specific biological questions! www.biorxiv.org/content/10.1...

biorxiv.org

MuSpAn: A Toolbox for Multiscale Spatial Analysis

The generation of spatial data in biology has been transformed by multiplex imaging and spatial-omics technologies, such as single cell spatial transcriptomics. These approaches permit a detailed mapp...

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Reposted by Josh Moore

Itai Yanai @itaiyanai.bsky.social · 25/12/2024

It’s crazy how talking with a science buddy is simultaneously what’s most likely to move the project forward and the thing that’s least prioritized in our schedule.

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Reposted by Josh Moore

James Balamuta @coatless.bsky.social · 15/12/2024

At long last... An official way to convert from office formats to #markdown with Microsoft's new {markitdown} #python package!!!! Next week's datathoning will be fun :) github.com/microsoft/ma...

A screenshot of the top half of the markitdown python package repository showing how to convert a microsoft excel spreedsheet into markdown.

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Reposted by Josh Moore

Andrew Mueller @sansseriff.bsky.social · 14/12/2024

If anyone ever needs a matplotlib plot in dark mode, I made a function that auto-converts most elements during export 🌙🧪 github.com/sansseriff/s...

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Reposted by Josh Moore

Joshua Bull @joshuabull.bsky.social · 13/12/2024

Sounds like what we need is something that makes it easier to generate quantitative, interpretable metrics that describe observable biological differences in tissue, without being a black box and requiring unreasonable amounts of training data... www.muspan.co.uk doi.org/10.1101/2024...

doi.org

MuSpAn: A Toolbox for Multiscale Spatial Analysis

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Reposted by Josh Moore

Joshua Bull @joshuabull.bsky.social · 10/12/2024

If you're at @oxfordcancer.bsky.social's #OxCODE this morning, go and chat to @josh-moore.bsky.social during the poster session! He's one of the key architects of MuSpAn and will be happy to answer any questions you may have about getting started with the software doi.org/10.1101/2024...

A picture of a poster about MuSpAn, a toolbox for Multiscale Spatial Analysis, at the OxCODE conference 2024

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Josh Moore @josh-moore.bsky.social · 09/12/2024

We’re thrilled to introduce MuSpAn! For researchers in biological imaging, MuSpAn provides tools for Multiscale Spatial Analysis with advanced mathematical methods. 🌟 For more information: www.muspan.co.uk 📝 Preprint: doi.org/10.1101/2024... We hope you find it as useful as we do! (Poster below)

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Reposted by Josh Moore

Joshua Bull @joshuabull.bsky.social · 21/10/2024

OK, I've taken a swing at it - a Mathematical Biology starter pack, please add (or remove) yourselves as necessary! (If that's possible? I have no idea how this works) go.bsky.app/GVkxwBv

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