This guy really dedicated his life to science: www.sciencedirect.com/science/arti... www.science.org/content/arti...

I am excited to share my first work in @schapirolab.bsky.social on Multiple Myeloma (MM) in collaboration with the Standal Lab from NTNU Norway. We use Imaging Mass Cytometry (IMC) on bone marrow biopsies from MM and precursor patients (details below): www.biorxiv.org/content/10.1...

Nature Method: Temporal and spatial omics technologies for 4D profiling www.nature.com/articles/s4...

And for anyone who has considered contributing to an open source package: don't be scared to propose changes. Even if it's not a complete and perfect solution, whoever is maintaining the package will help you in get to the right solution and they will be incredibly grateful.

For people like me who don't have a team behind a package like CellCharter, contributions like these mean a lot. So thank you Lukas :) And congratulations, it's not always easy to jump into an existing codebase and propose changes.

RCS measures how large a cell niche (aka spatial domain aka spatial cluster) is compared to what would be normally expected. This pushed me to completely rewrite the system for generating and plotting boundaries for cell niches. The new system is now more efficient, consistent, and visually clear.

A few weeks ago, we released CellCharter v0.3.5. Among some bug fixes, we received our first contribution from an external contributor: @loggas.bsky.social ! He designed a new metric called Relative Component Size (RCS).

Spotted: @loggas.bsky.social and @arojhada.bsky.social teaching phenotyping to our Advanced Systems Biology students

🖥️🧬 I used to have to tell my students not to bother with differential expression analysis in a language outside of R. Recently, with pydeseq2 and now InMoose, this is changing! bmcbioinformatics.biomedcentral.com/articles/10....

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...

An alternative to tSNE & UMAP for more accurate data visualization: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data. The trees are constructed to accurately represent true distances between the objects in the high-dimensional space.

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

And it's finally here! napari 0.6.0 is out on PyPI and conda-forge! 🥳 We've had a few threads about this release already but let's recap with some highlights: 🧵

Big updates for the Nextflow @vscode.dev extension! 🚀 🔍 Workflow view – Visualize logical structure of pipelines ⚙️ Process view – See all processes in one place 🌐 Seqera view – Manage connected CEs directly in the IDE 📚 Resources view – Quickly access Copilot, AI tools & training

Miso made in space tastes nuttier! Researchers successfully make miso at the #InternationalSpaceStation, confirming that making fermented foods in space is possible. www.cell.com/iscience/ful... @medialab.bsky.social Maggie Coblentz @novo-nordisk.bsky.social Joshua D. Evans @cp-cell.bsky.social

Super excited to finally see this published! Our new method to use combinatorial staining and deep learning to push the multiplexing boundaries of spatial proteomics!

Science is an investment that pays enormous dividends. So if you’re business-minded, it’s an offer you can’t refuse! Here's my full speech from the Stand Up For Science rally in DC today: www.youtube.com/watch?v=eemj...

🧵 We are excited to share our new paper, showcasing micronuclAI, which leverages #AI and #ComputerVision to detect #chromosomal_instability #CIN #micronuclei Congratulations to @miguelib.bsky.social and Lindsay Caprio for leading this project.

The March issue is out! This week: TOX-inducible-KO 🐁show how #TOX maintains #exhausted CD8 #Tcell epigenetic fate; visualizing temporal & spatial #STING expression; & UVB-driven #mitochondrial Z-🧬complexed w ZBP1 fuels #autoimmune #photosensitivity via cGAS-STING! science.org/toc/sciimmunol/10/105

In an unprecedented move, the US National Institutes of Health has begun mass terminations of research grants that fund active scientific projects because they no longer meet “agency priorities”. https://go.nature.com/4bpG2It

One week to go!

Does anyone have a good universal membrane marker besides NaKATPase and CD98, that ideally stains epithelium/cancer similarly strong as stroma/immune cells? Antibody will be used for spatial proteomics (cyclic IF), goal is a good whole cell segmentation downstream

Gemini Code Assist now free: blog.google/technology/d... VSCode: marketplace.visualstudio.com/items?itemNa... Positron: open-vsx.org/extension/Go... #Rstats

Society, patients and clinicians welcome a much-needed non-opioid pain medication. Vertex’s first-in-class analgesic Journavx could soon be followed by a new generation of addiction-free pain drugs acting at NaV1.8 sodium channels www.nature.com/articles/s41...

Post-doc opening to join our lab @ebi.embl.org to develop&apply #bioinformatics and #machine-learning methods to study intra-/extra cellular networks to extract disease mechanisms from #single-cell and #spatial multiomic data - please share 🙏 : embl.wd103.myworkdayjobs.com/EMBL/job/Hin...

Are you a postdoc at @uniheidelberg.bsky.social? Don't forget to sign up!

Much of my understanding came from his amazing video by 3Blue1Brown: www.youtube.com/watch?v=m2MI...

2025 looking great so far!

Huji Xu is a physician and researcher who took a chance on a revolutionary approach to treating autoimmune disease. Xu is part of Nature’s 10, a list of people who shaped science in 2024. 🧪

Build common reference indexes with Nextflow @nf-co.re nf-core/references https://github.com/nf-core/references 🧬🖥️🧪

Any popular benchmark will become a target for AI companies. A chart of ARC-AGI scores for past five years of OpenAI models (updated w/ release dates), as provided by Riley Goodside.

Laser tag lab edition #happyholidays 🎄🎁🎅🏼

Schapiro lab does #ESSB 🔬🍷

Thank you to the organisers Anja Hauser, @denisschapiro.bsky.social, @schuerch.bsky.social and the wider team who have made the 1st #ESSB Symposium a reality! We have greatly enjoyed the meeting.

@loggas.bsky.social - Poster 72

Vision foundation models for microscopy from Lundberg lab - first proteome-wide hierarchical map of proteome organization that is learned from image data. #science 🧪 www.biorxiv.org/content/10.1...

Formulaic is the go-to way to specify design formulas in Python, e.g. ~treatment + timepoint. To compare sth, one needs to specify a contrast, e.g "on treatment vs baseline". To make this easier, we developed "formulaic-contrasts": formulaic-contrasts.readthedocs.io/en/latest/

MuSpAn: A Toolbox for Multiscale Spatial Analysis https://www.biorxiv.org/content/10.1101/2024.12.06.627195v1

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)

I could not be more thrilled to announce the Nature Methods @naturemethods.bsky.social Method of the Year is Spatial Proteomics! Please see our editorial as a roadmap to the fantastic content in this special issue! www.nature.com/articles/s41...

🔬 Spatial omics: revolutionary breakthrough or just incremental progress? In the third Batch Effect blog post, I compared this emerging technology to the historic hype around interferon therapy. Is this time going to be different? www.batcheffect.com/p/breakthrou...

Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨 We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research! Read more: bmcgenomics.biomedcentral.com/articles/10.... 1/8

Rather than immune suppression, CD206+ TAMs recruit a tumor-reactive network of CD8 T cells, cDC1s, and NK cells doi.org/10.1084/jem.... @maxkrummel.bsky.social @jexpmed.bsky.social

While we are all discussing sc/snRNAseq quality control metrics thanks to the recent BMC Genomics paper, I also want to take a moment to point to the related work by Zoe Clarke and Gary Bader. Preprint: www.biorxiv.org/content/10.1... Slides: f1000research.com/slides/13-1255

We are looking for a Postdoc with a strong computational background to join our team. Want to work on the development and application of computational methods in the field of translational spatial biology? Apply now! karriere.klinikum.uni-heidelberg.de/index.php?ac...