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Martin Emons

@martinemons.bsky.social
131 followers 257 following 15 posts

PhD student in Statistical Bioinformatics at University of Zurich and SIB

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Reposted by Martin Emons
Mark Robinson @markrobinsonca.bsky.social · 24/08/2026
That's exciting. From a hackathon in December 2023 (spatialhackathon.github.io/past.html) to a preprint in June 2025 (www.biorxiv.org/content/10.1...) to this publication out today (doi.org/10.1038/s415...).
spatialhackathon.github.io
Past Events
Github Pages for SpatialHackathon
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 18/08/2026
scDblFinder in Python with GPU support www.biorxiv.org/content/10.64898/20…
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Matthias Meyer-Bender @matthiasmeybe.bsky.social · 24/07/2026
🚀 Our paper on spatialproteomics is now out in @natmethods.nature.com Spatialproteomics is a Python package for analyzing highly multiplexed immunofluorescence imaging data. Built on xarray and dask, with seamless integration into the scverse ecosystem. www.nature.com/articles/s41...
Spatialproteomics is a Python package for end-to-end processing and analysis of highly multiplexed immunofluorescence imaging data. Built on xarray and dask, with seamless integration into the scverse ecosystem.
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Pierre-Luc Germain @plger.bsky.social · 23/06/2026
How do >1600 transcription factors (TFs) bind across hundreds of cell types? Experimentally profiling every combination isn't practically doable. But relying on DNA motifs isn't a great alternative -- they lack both sensitivity and specificity. #Genomics #GeneRegulation 👇
Motifs are poor proxies for binding
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Nav @naveed-ishaque.bsky.social · 18/06/2026
Cell segmentation for spatial transcriptomics isn’t so easy, right? We thought so too. A wonderful group lead by @garybader.bsky.social and @rgottardo.bsky.social put together a perspectives piece on where things stand, the challenges, and what’s next. Check it out: arxiv.org/pdf/2606.09675
arxiv.org
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Martina Morchio @martina-m.bsky.social · 19/05/2026
Just analysed 48 single nuclei samples with scprocess and went from fastq files to cell-type annotation in a couple of weeks!! Really recommend this pipeline developed by @willmacnair.bsky.social and team, thank you for making it public!! github.com/marusakod/sc...
github.com
GitHub - marusakod/scprocess: Snakemake pipeline for processing single cell data
Snakemake pipeline for processing single cell data - marusakod/scprocess
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Mark Robinson @markrobinsonca.bsky.social · 06/05/2026
This was a fun effort from our lab retreat (!) to recreate a "arms-length" benchmark (i.e., one that someone else created) using our Omnibenchmark framework. We all learned a lot in the process ..
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Martin Emons @martinemons.bsky.social · 16/04/2026
We are excited to share our latest preprint on spatialFDA, a method for the statistical analysis of spatial omics data. bioconductor.org/packages/3.2...
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EMBL-EBI Training @training.ebi.embl.org · 16/02/2026
Join us next week for the second free webinar in our spatial transcriptomics series: www.ebi.ac.uk/training/eve... Daria Lazic (EMBL Heidelberg) presents 'Imaging-based spatial transcriptomics: methods, preprocessing, and quality control' on 25 February | 14:30 UK time.
Webinar at EMBL-EBI: "Imaging-based spatial transcriptomics: methods, preprocessing, and quality control". 25-02-2026, 14:30-15:30 GMT. Speaker (with photo): Daria Lazic, EMBL Heidelberg
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Stephen Turner @stephenturner.us · 12/02/2026
Omnibenchmark (omnibenchmark.org): transparent, reproducible, extensible and standardized orchestration of solo and collaborative benchmarks arxiv.org/abs/2409.17038 🧬💻🧪
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 21/11/2025
Orchestrating Spatial Transcriptomics Analysis with Bioconductor www.biorxiv.org/content/10.1101/202…
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Reposted by Martin Emons
Samuel Gunz @samuelgunz.bsky.social · 14/10/2025
I'm very excited to share our latest preprint! We introduce structure-based analysis of spatial omics data – an approach that focuses on multi-cellular anatomical structures rather than single cells. We also present sosta to facilitate this type of analysis: bioconductor.org/packages/sos...
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Martin Emons @martinemons.bsky.social · 11/09/2025
We are excited to share the publication of our paper on exploratory spatial statistics for spatial omics data academic.oup.com/nar/article/...
academic.oup.com
Harnessing the potential of spatial statistics for spatial omics data with pasta
Abstract. Spatial omics allow for the molecular characterization of cells in their spatial context. Notably, the two main technological streams, imaging-ba
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Martin Emons @martinemons.bsky.social · 27/06/2025
Update: We greatly revised our paper and renamed it “Harnessing the Potential of Spatial Statistics for Spatial Omics Data with pasta”. We discuss the broad range of exploratory spatial statistics options for spatial Omics technologies and show relevant use cases. arxiv.org/abs/2412.01561
arxiv.org
Harnessing the Potential of Spatial Statistics for Spatial Omics Data with pasta
Spatial omics assays allow for the molecular characterisation of cells in their spatial context. Notably, the two main technological streams, imaging-based and high-throughput sequencing-based, can gi...
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