🧵 See 👇 our new preprint on shared and organ-specific gene expression programs of fibrotic diseases 🧬

📄 Paper: doi.org/10.64898/202...

📊 Explore the data: organfibrosis.saezlab.org

Was lovely to see many of you @ I2K! Despite having major FOMO about missing so much stuff this fall (GloBIAS! CytoData! FoundingGIDE! CBIAS!), conferences ARE usually a great way to find @erinweisbart.bsky.social and I. In Episode 19, we talk through great societies/meetings we think you'll enjoy!

Today is the last chance to register for #CytoData2025. Don’t miss a fantastic program covering the full spectrum of image-based profiling!

cytodata25.eu-openscreen.eu

New work from Iva Buljan @ivabuljan.bsky.social in our lab!
We mapped how human tissue architecture changes with age using ~25k histology slides from 983 donors.
This is the first body-wide atlas of human microanatomy.
📄 Preprint: www.biorxiv.org/content/10.1...

🙏 Thanks to all collaborators at the DKFZ, UKHD and Heidelberg University, and UKE Institute of Pathology, to the patients, and funders.
@saezlab.bsky.social
@dkfz.bsky.social
@dkfz-iic.bsky.social
@tanevski.bsky.social
@struxa.bsky.social
@hlsalliance.bsky.social
@erc.europa.eu
@helmholtz.de
5/5

Our analysis reveals distinct recurrent CRC trajectories:
🤝 Tumor-CAF metabolic cooperation with immune shielding
🔥 Glycolytic shift with vascular remodeling and myeloid enrichment
Same disease, different mechanisms, suggesting different treatment responses.
4/5

GitHub - HartmannLab/MuVIcell: From cell-type stratified features to multicellular coordinated programs From cell-type stratified features to multicellular coordinated programs - HartmannLab/MuVIcell

🧩 To identify which changes co-occur in patients, we built MuVIcell, an open-source Python package that applies the MuVI factor analysis framework to model all spatial, metabolic, morphological, and compositional features per cell type.
Try it yourself: github.com/HartmannLab/...
3/5

⏳ What shifts with pT stage?
Early lesions show high proliferation and fatty acid oxidation capacity. Later, glycolysis rises, stroma and vasculature reorganize, and lymphocytes give way to myeloid cells. Spatial architecture predicts stage better than composition or metabolic state.
2/5

Robust multicellular programs dissect the complex tumor microenvironment and track disease progression in colorectal adenocarcinomas Colorectal cancer (CRC) is highly heterogeneous, with five-year survival rates dropping from $\sim$90% in localized disease to $\sim$15% with distant metastases. Disease progression is shaped not only...

🧭 Colorectal cancer doesn’t follow a single path.
Using spatial proteomics on ~500 tumors, we found distinct trajectories from early to late stage, involving the whole tumor microenvironment and its metabolic state.
📄 Preprint: arxiv.org/abs/2510.05083
#SpatialBiology #CRC #ImageBasedProfiling
1/5

We present our MetaProViz #Rpackage for #metabolomics analysis & prior knowledge integration to generate mechanistic hypotheses on how metabolic changes affect metabolite classes, pathways & environment interaction

🔗
www.biorxiv.org/content/10.1...

📦
saezlab.github.io/MetaProViz/

🧵 Thread ⬇️

EMBL-EBI-Sanger postdoctoral fellowships (ESPOD) The ESPOD fellowship builds on the collaborative relationship between EMBL-EBI and the Wellcome Sanger Institute, offering projects that combine experimental (wet-lab) and computational (dry-lab) appr...

Check out this opportunity to join my lab as a postdoc! www.ebi.ac.uk/research/pos...

Every year, faculty from EMBL-EBI and the Wellcome Sanger Institute co-develop projects that allow fellows to be part of ✨both✨ of these amazing research institutes.

This project has been in the making for quite some time. CORNETO not only integrates key concepts and methodologies in biological network inference, but also introduces a novel framework for multi-condition analysis. Congrats to the team, and especially to @pablormier.bsky.social for leading this.

𝗢𝗻𝗲 𝗪𝗲𝗲𝗸 𝗟𝗲𝗳𝘁: Abstract submission for oral presentations 🗣️ and hackathon registration 🧑‍💻 for CytoData 2025 Berlin close July 25!

Submit abstracts or register here: 🔗 cytodata25.eu-openscreen.eu/registration/

#Cytodata2025 #Hackathon #ImageBasedProfiling

🔬API-first feature extraction for image-based profiling workflows

If you need to obtain interpretable features from your segmented microscopy images, but want to do it in a fully automated way, we know the struggle.

1/6

Exciting news! We've extended the deadline for oral submissions for Cytodata 2025. You now have until July 25 to submit oral presentations and register for the hackathon. Don't miss this chance! Poster submission closes September 10, and general registration ends October 1

🌟 𝗥𝗲𝗺𝗶𝗻𝗱𝗲𝗿 🌟
The deadline for abstract submissions for oral presentations at Cytodata 2025 in Berlin is approaching!

👉 𝗦𝘂𝗯𝗺𝗶𝘁 𝘆𝗼𝘂𝗿 𝗮𝗯𝘀𝘁𝗿𝗮𝗰𝘁 𝗯𝘆 𝗝𝘂𝗻𝗲 25!
cytodata25.eu-openscreen.eu/registration/

#BerlinConference #Imageanalysis #Microscopy

Join us in Berlin for CytoData 2025!
👉 Info & registration: cytodata25.eu-openscreen.eu

🔬 Hackathon: Nov 17–19
📢 Symposium: Nov 20–21

Explore advancements in image-based profiling & high-content screening and Tackle real-world challenges using EU-OPENSCREEN data.

Open Positions CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences

🚨 3 days left to apply!
Join us at CeMM (Vienna) to work on AI + computational pathology projects like LazySlide.
Amazing team, H100 GPUs, real impact.
Apply now: cemm.at/join-cemm/op...

If you need to compare profiles across many conditions or perturbations, have a look!

Ever wondered which method to use to infer kinase activities from phosphoproteomics data? 💻💭Our revised comprehensive evaluation of kinase activity inference tools, done in collaboration with the Zhang lab @bcmhouston.bsky.social, is now out @natcomms.nature.com 🔬 tinyurl.com/4twuc6z4

A multilayer network approach elucidates time- and tissue-specific developmental and aging processes Understanding the dynamic interplay of proteins across different life stages and tissues is essential for deciphering the molecular mechanisms underpinning development, aging, and disease. Here, we pr...

Have you ever wondered how protein interactions change across tissues and over time?
#networkmedicine #development #aging
👇 Check what we found under the incredible mentorship of
#menchelab & @andre-rendeiro.com :
www.biorxiv.org/content/10.1...

If you're interested in finding recurrent spatial patterns in your tissues, now is a good time to check out Kasumi!

PhD/Postdoc in Spatial Omics for Cardiology Post a job in 3min, or find thousands of job offers like this one at jobRxiv!

We have an opening for a PhD/Postdoc in Spatial Omics for Cardiology in Heidelberg 🫀 #job #academicjob #phd #postdoc #cadiology 👇
jobrxiv.org/job/heidelbe...

Registrations are open for the best scientific event of the year!
Source: my very unbiased and authoritative opinion 😂

Join us in Berlin in November to discuss the best ways to go from images to biological insight and new treatments.

🚨 New preprint: Topography Aware Optimal Transport for Alignment of Spatial Omics Data

We present our new alignment framework TOAST www.biorxiv.org/content/10.1...

Congrats & Good luck to our @slobentanzer.bsky.social as he starts his group @diabresearch-dzd.bsky.social & @comphealthmunich.bsky.social - he is hiring 👇

Reprogramming site-specific retrotransposon activity to new DNA sites - Nature A study of retrotransposon activity repurposes a retroelement called R2Tocc to create a programmable system called STITCHR that enables diverse genome edits including efficient, scarless large pa...

So excited to share our new paper out today in @nature.com. We repurposed R2 retrotransposons to create STITCHR, a tool that can make virtually any kind of edit in mammalian genomes including the scarless multi-kilobase scale insertions 🧵

www.nature.com/articles/s41...

Interested in supporting the advancement of image-based profiling? Want to shape how large cell and tissue image datasets will be analyzed in the future? Please consider hosting CytoData!

Ask Erin, Dear Beth On Ask Erin/Dear Beth, bioimage analysis experts Beth Cimini and Erin Weisbart, of the Imaging Platform at the Broad Institute of MIT and Harvard, answer your image analysis questions! Whether it’s ab...

Delighted to announce that @erinweisbart.bsky.social and I have teamed up to create a new bioimage analysis video podcast called Ask Erin/Dear Beth - you can check it out at the link below! It will highlight common challenges in #bioimageanalysis, as well as our favorite solutions to them. (1/x)

Big news, you can now follow the CytoData society on BS and get even more image-based profiling in your timeline 🤓