Michele Bortolomeazzi, Christian Schmidt and Jan-Philipp Mallm at @nfdi4bioimage.bsky.social have developed a new OMERO-web plugin: OMERO-vitessce. It enables the visualization of datasets hosted in #OMERO with the #Vitessce multimodal data viewer.
Find the poster here:
👉 zenodo.org/records/1483...

What a special atmosphere! #ELMI2025 Poster Session 1 on Helix A last night. The perfect environment to exchange with friends & colleagues about #bioimaging #RDM:
- OMERO-vitessce
- IO-FAST initiative
- @nfdi4bioimage.bsky.social Data Stewardship
Talks, Workshops & Poster Session 2 up ahead today!🔬

Want to visualize & create a website for your omics data (incld CITEseq, scATACseq, #SpatialTranscriptomics)?

Try ShinyCell2!😆

Compatible with data formats Seurat Signac ArchR Scanpy

vs cellxgene WebAtlas Vitessce

github.com/the-ouyang-l...

bioRxiv 2024
www.biorxiv.org/content/10.1...

Vitessce
Integrative visualization of multimodal & spatially resolved single-cell data

vitessce.io

Python/R/Java/online configuration editor

Support multiple data types/file formats
SpatialData AnnData MuData CSV OME-TIFF OME-Zarr

@naturemethods.bsky.social 2025
www.nature.com/articles/s41...

@mkeller7.bsky.social Sonja Stockhaus @wvierdag.bsky.social @lucamarconato.bsky.social
We started working on developing common view-configurations based on Vega, to improve reproducibility of plots and allow for displaying the same visualization in spatialdata-plot, #napari and #vitessce.

Build your own online integrated platform for single-cell & spatial transcriptomic data using WebAtlas pipeline

Cell2location
StabMap
Unify image & gene expression files into Zarr format
Compatible with SpatialData
Based on Vitessce framework

#Naturemethods 2024
www.nature.com/articles/s41...

This week's recap highlights protein design with RoseTTAFold, surveillance with wastewater sequencing, T2T human genomes, Vitessce for visualization of multimodal spatial single-cell data, and Taxometer for taxonomic classification of metagenomics contigs... blog.stephenturner.us/p/weekly-rec... 🧬🖥️

We additionally developed web-based Vitessce apps for exploring each of these datasets freely on your browser! I'm a big fan, so please check them out! You can find them along with the analysis and links to raw data files on the landing page for our github repo. 11/12 github.com/LieberInstit...

Join us next Monday for a talk by Mark Keller from
@harvardmed.bsky.social! 🌟

📊The Vitessce framework for interactive visualization of single-cell data and its applications

⏱️ 5 May, 1 pm (AEST)
🔗 bit.ly/4hZLxiR

We also created an interactive website so doctors and scientists can easily explore our research data and use it to advance care and discovery.

Try it out for yourself: jef.works/vitessce-col...

Work led by post-doc Sami Singh with Hamid Rabb + team 🎉 7/7

Join us next week for the fourth #webinar in our
#SpatialTranscriptomics series, where we will talk about how to visualise spatial transcriptomics data using napari and Vitessce.

Registration is free but essential: www.ebi.ac.uk/training/eve...

🖥️🧬

(2/3) The hands-on sessions provided valuable experience in analyzing #spatially resolved #transcriptomics, #proteomics, and #metabolomics data. We gained practical skills using key tools and pipelines, including #Harpy, #Cardinal, and interactive visualization with #Napari and #Vitessce.

https://vitessce.io/ Integrative visualization of multimodal and spatially resolved single-cell data 🧬🖥️
Paper: https://www.nature.com/articles/s41592-024-02436-x
Code: https://github.com/vitessce/vitessce
Py 📦 https://pypi.org/project/vitessce/
#Rstats 📦 https://github.com/vitessce/vitessceR

orth, et al.: Vitessce Link: A Mixed Reality and 2D Display Hybrid Approach for Visual Analysis of 3D Tissue Maps https://arxiv.org/abs/2511.04262 https://arxiv.org/pdf/2511.04262 https://arxiv.org/html/2511.04262

🧠 Curious what KPMP tissue looks like up close?

Use our Spatial Viewer to explore kidney imaging datasets interactively in Vitessce.

No login needed — just click and explore:

🔗 atlas.kpmp.org/spatial-view...

#KPMP #spatialdata #kidneyresearch #dataviz

Have a look at our notebook anndata.readthedocs.io/en/stable/tu... to learn more, featuring data hosted by the @ngehlenborg.bsky.social's HIDIVE lab that can be directly visualized using Vitessce at this link: tinyurl.com/jtan4nx7