Neutrophils are the most abundant immune cell in our body, and also one of the strangest. Your body makes around 1 billion of them per kg of body weight every day, they live only 12 to 24 hours, and they roll along blood vessels under forces 10 times higher than any other immune cell can survive.

Neutrophils are weird (Part 1): rolling and squeezing

How neutrophils are made, how they move, and why they were missing from our datasets

open.substack.com

🚀 Hevelion, une start-up issue de @fbm-unil.bsky.social @unil.bsky.social, développe un outil «omique» pour la #cartographie des cellules et de leurs interactions, notamment en #oncologie. Lire la rencontre avec son fondateur @marcovarrone.bsky.social 🔗 www.unil.ch/news/fr/1763... #SpatialOmics

Hevelion, une start-up à l’ambition « spatiale »

Soutenue par le FNS et par une bourse de la Fondation pour l’innovation et la technologie, la jeune pousse issue de l’Unil développe un outil « omique » pour la cartographie des cellules et de leurs i...

unil.ch

I collected all of what I could find about the upcoming Illumina Spatial Transcriptomics technology, with some predictions about costs and sensitivity compared to 10x Genomics Visium HD www.batcheffect.com/p/the-giant-...

The giant wakes up: Illumina goes spatial

Predictions on the upcoming Illumina spatial transcriptomics technology

batcheffect.com

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).

GitHub - CSOgroup/cellcharter: A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.

A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data. - CSOgroup/cellcharter

github.com

After 6 (healthy) months of hiatus from social media, first post with a brand new conference announcement!! 🔥COMPUTATIONAL BIOLOGY IS EVERYWHERE! Join us in Lausanne for the first international Computational Biology Symposium! 18-19 September 2025 Registrations are OPEN! cbiosymposium.unil.ch

Last year I completed my PhD and my father recorded my public defense 📹 So I decided to share it! I talked about the communities of cells in our bodies and how we develop algorithms to study them. Hope you enjoy it!

Computational models to characterize spatial intra-tumor heterogeneity | Marco Varrone

YouTube video by Marco Varrone

youtu.be

The only sort of gatekeeper I wish we saw more of were those who wanted better software. Who cares if your model performs the best if it's unusable, or if your pipeline aligs reads faster if it only works on your local work computer? Or if there's no documentation on how to use any of it.

The scverse ecosystem is one of the best things that could have ever happened to the single-cell and spatial fields. Smoother computational analyses mean faster and better research

scverse@scverse.bsky.social · 2y ago

Closing 2024, scverse celebrates growth and collaboration! Huge thanks to everyone on this journey and our core team & board (@fabiantheis.bsky.social, @francescafinotello.bsky.social, @steglelab.bsky.social, Nir Yosef, @panosroussos.bsky.social, @robp.bsky.social). Here's to an inspiring 2025!

Contributing to this project has been very cool! Quick tip for anyone interested in cell segmentation: I started with StarDist but it failed to detect nuclei in samples with regions of very different cell density. Switched to DeepCell Mesmer and it worked like a charm!

Elisa Oricchio@elisaoricchio.bsky.social · 2y ago

Just before the holidays, here is the latest from the Oricchio lab. In collaboration with the hemato-oncology team, we established a new model to test therapies on lymphoma patient samples by preserving the tissue composition and architecture of the original tumors. www.nature.com/articles/s41...

To bring to light data science topics that usually don’t make it into publications I started a blog on this topic: hrovatin.github.io By interviewing different researchers, I plan to find out what is going on in the community.

We are used to thinking that, when an organism has cancer, all other cells will fight it. We are now realizing that this is not true, and some of these cells may even help it. In the fourth Batch Effect post I talked about 4 aspects:

The hidden allies of cancer

How spatial omics is bringing normal cell interactions into focus

batcheffect.com

🔬 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...

Breakthrough or incremental progress?

Why spatial omics is revolutionary for biology and medicine

batcheffect.com

What do fruit pies 🥧, lego sets🧩, and cities🏙️ have in common? They are all metaphors used to describe spatial transcriptomics. In the second Batch Effect blog post I explored the best metaphor to make anyone understand what is spatial transcriptomics www.batcheffect.com/p/the-best-m...

The best metaphor for spatial transcriptomics

How everyone can understand what is spatial transcriptomics

batcheffect.com

If you are considering creating a Python package I strongly suggest cookiecutter-scverse by @scverse.bsky.social It’s a template that already incorporates many useful features. github.com/scverse/cook...

The Human Cell Atlas: towards a first draft atlas. I often read people complaining about "yet another atlas" published, but they are an important component of modern cell biology. They drive discovery, enable reproducibility, and I use them in nearly every project I work on.

The Human Cell Atlas: towards a first draft atlas

In a collection of research articles and related content, the Human Cell Atlas consortium presents tools, data and ideas towards the generation of their first draft atlas of cells in the human body.

nature.com

A few months ago, I started Batch Effect, a blog on the latest in cancer research under the lens of computational biology and spatial omics. I never shared here, so I'll start posting one old article every week. Hopefully we'll catch up just in time for a new series I am working on!

Welcome to Batch Effect

A blog on the new frontiers of Computational Biology for cancer research

batcheffect.com

🎉 We released CellCharter v0.3.2! - Now part of the Scverse ecosystem - More efficient differential neighborhood enrichment - Peak finding for cluster stability - Compatible with the latest PyTorch A few lessons learned along the way 🧵 1/4 github.com/CSOgroup/cel...

GitHub - CSOgroup/cellcharter: A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.

A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data. - CSOgroup/cellcharter

github.com

Excited that our paper "CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity" is finally out! CellCharter is a computational framework to identify and study cellular niches in large-scale spatial transcriptomics, proteomics, and even epigenomics data.

CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity - Natu...

CellCharter is a flexible, platform-agnostic method for identifying cell niches in spatially resolved data. Analysis of lung cancers demonstrates the importance of considering spatial information, exe...

nature.com

Hello there 👋 I'm Marco, a computer engineer turned computational biologist. In my PhD I'm currently exploring spatial omics data to study cancer. I have learned a lot about it in the last 3 years and I would love to share it, but I still don't know in which format (posts, blogs or videos).