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...
🧪🧬🔬💻
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 👀
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 🧬🧪👨🔬
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
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)
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
If you have any queries about either roles, please feel free to dm me
hash-dump:
#spatialbiology #academicjobs #postdoc #mathmodelling #jobs #crc #dataanalysis #spatialtrancriptiomics
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
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!
...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!)
Just to clarify, bribery is well received!
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
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...
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...
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...
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.
A screenshot of the top half of the markitdown python package repository showing how to convert a microsoft excel spreedsheet into markdown.
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...
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...
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...
A picture of a poster about MuSpAn, a toolbox for Multiscale Spatial Analysis, at the OxCODE conference 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...
Please do! And if you have any questions let us know 👍🏻
Massive props go to @joshuabull.bsky.social for making this a really fun project to work on
A poster giving an overview of MuSpAn.
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)
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
