📢 APAC researchers — showcase your work in the @10xgenomics.bsky.social Visium HD 3' Art Gallery!

Submit your image by 30 Nov 2025 to receive:
✅ 50% off your next Visium HD 3' product (all participants)
🎨 Global spotlight + future swag features

👉 Apply: 10xgen.com/1NK

#SpatialBiology #VisiumHD

See how the #VisiumHD 3’ whole transcriptome assay powers comprehensive spatial characterization of the tumor microenvironment in our #AACR2025 poster. https://bit.ly/46Q9d6w

Happening in 1 week - register now! 🧬🔬💻

t.co/xvejAtykmk

#Visium #VisiumHD #Xenium #SpatialTranscriptomics #SpatialBiology #InSituSequencing

📢 NEW! Visium HD 3’ + Long Reads from @10xgenomics.bsky.social

Explore whole transcriptome spatial analysis at single-cell resolution. Now sequence full-length transcripts to uncover isoforms & SNVs.

👉 Protocols: shorturl.at/E3A4G

#SpatialTranscriptomics #VisiumHD #LongReadSeq #ONT #PacBio

On 9/16 at 2PM, join #DukeMGC & @10xgenomics.bsky.social to explore how #VisiumHD and #Xenium platforms are advancing #spatialbiology!

REGISTER HERE: docs.google.com/forms/d/17HI...

Contact bryan.hess@10xgenomics.com or #DukeMGC Assistant Director, karen.abramson@duke.edu with any questions.

Take your #VisiumHD 3' studies to new lengths with long reads! Map isoforms, expressed SNVs, and more with Oxford Nanopore and PacBio sequencing for even greater discovery power. New compatible protocols now available: https://bit.ly/3JORwLH

Using #VisiumHD & #XeniumInSitu, NIH scientists led by Jeremie Oliver Piña discovered a new role for PAX9 in palate formation, offering valuable insights into cleft palate disorders. Read more: www.nature.com/articles/s41...

Fin‑tastic news: #VisiumHD 3' is species‑agnostic (yes, zebrafish!). Hop to the #10xGenomics website and check the #dataset yourself!

Gill‑ty of bulk RNA?

🐠 Go spatial!
🐡 Scale up your story!
🐟 Remember, Danio is in the details!

Link to the dataset is in the first comment.

Join our webinar on the new #VisiumHD 3’ assay to explore spatial transcriptomics and the technical aspects of the platform. This session offers practical insights and examples for both beginners and experienced users looking to optimize spatial experiments. Register at bit.ly/3How6E6

We’re shipping the #VisiumHD 3’ assay! Learn how to bring species-agnostic, whole transcriptome spatial analysis at single cell scale to your lab, including new cell segmentation capabilities compatible across all HD products: bit.ly/4mPrGX5

#SpotSweeper is now published!

Check our journal club session summary of the pre-print version by @lahuuki.bsky.social

The new features @boyiguo.bsky.social + @mictott.bsky.social added in this revised manuscript enhance the use cases for #SpotSweeper: 👀 #VisiumHD data!

youtu.be/f72XcXmtkfw?...

How mapping the spatial biology of the tumor microenvironment can benefit cancer drug discovery and development - 10x Genomics Spatial transcriptomics reveals complex and therapeutically relevant interactions among tumor and immune cells in the TME and tumor boundary.

Read the blog to learn how 10x scientists used the #Chromium single cell, #VisiumHD and #Xenium platforms in human colorectal cancer to localize anti-tumor macrophage subtypes and clonally expanded T cells in the TME: bit.ly/4439Xnu

It’s an honor to see our publication in @natureportfolio.nature.com! Read the blog to learn how 10x scientists used the #VisiumHD and #Xenium platforms in human colorectal cancer to localize anti-tumor macrophage subtypes and clonally expanded T cells in the TME: bit.ly/4439Xnu

KODAMA goes spatial.
doi.org/10.1101/2025...
#spatialtranscriptomics #visium #visiumhd #seurat #giotto

The new #VisiumHD 3’ assay expands the possibilities for spatial discovery. Join our webinar to see how you can explore the whole transcriptome at #singlecell–scale resolution across species. Register today: bit.ly/3FfaEk9

Meet the newest member of the #VisiumHD family! We’re excited to bring you a species-agnostic, whole transcriptome spatial discovery solution with the Visium HD 3’ assay—now at true single cell resolution with our cell segmentation software: bit.ly/4kaTrqJ

Species-agnostic poly-A based #VisiumHD is here!!!

Now you can use the most reliable #10xGenomics whole transcriptome #spatialtranscriptomics at single cell scale on fresh frozen samples of your species of choice.

#RNA #transcriptomics #spatialbiology #tissue #histology #pathology #cancer

Day 1 of #AGBT25, ft. exciting @10xgenomics.bsky.social announcements!

Later this year, #Flex coming out with 96 barcodes then eventually scaling up to 384, #Xenium #protein capabilities, and #VisiumHD #cellsegmentation.... #DukeMGC can't decide which we're most excited about! 🧬🧠💻

#visiumhd product updates : segmentation , visium HD XL , visium hd 3’ @10xgenomics.bsky.social #agbt25

Granzyme K+CD8+ T cells interact with fibroblasts to promote neutrophilic inflammation in nasal polyps - Nature Communications Chronic rhinosinusitis with nasal polyps generally has a type 2 inflammatory eosinophilic profile but can have a treatment resistant neutrophilic phenotype. Here the authors characterise nasal polyps ...

Congrats to China researchers on their groundbreaking study of chronic rhinosinusitis with nasal polyp using #Chromium & #VisiumHD to identify a unique subset of cells for potential new targeted treatments for neutrophilic inflammation & therapy resistance!

Systematic Benchmarking of High-Throughput Subcellular Spatial Transcriptomics Platforms Recent advancements in spatial transcriptomics technologies have significantly enhanced resolution and throughput, underscoring an urgent need for systematic benchmarking. To address this, we collecte...

The heroes we need and don't deserve - a great benchmarking resource comparing BGI's #stereoseq with @brukercorporation.bsky.social 's #CosMX 6k and @10xgenomics.bsky.social #VisiumHD and #Xenium 5k - Packed with lots of interesting metrics and observations, including transcript diffusion...

Lei has also used #RCTD by Cable, @rafalab.bsky.social et al

To use it you need to have a reference single cell dataset

They have used #RCTD to integrate single cell and #VisiumHD data 📊. Doing so helped them check whether their Visium HD clusters were ok

SpatialBiologyWestCoastUS2024

Today at #SpatialBiology West Coast US 2024 I'll be sharing some of the lessons we've learned since 2019 analyzing 🧐 #Visium & more recently #VisiumHD #SpatialTranscriptomics data 🧬 with my colleagues at @lieberinstitute.bsky.social & @jhubiostat.bsky.social

speakerdeck.com/lcolladotor/...

VisiumHD: From 16 µm to 2 µm resolution — sainsc 0.2.2.dev5+g0c33c57 documentation

Have you performed a #VisiumHD run, and frustrated that you had to analyse data in 8/16 um bins?
We just updated #Sainsc to create maps of cell types at 2 um resolution for #VisiumHD: sainsc.readthedocs.io/tutorials/tu....
Check it out and let us know - happy to add features/fixes.

Photo of Margaret McFall-Ngai’s talk as part of the Ernst Mayr Lecture series.

I’m on vacation but I ended up crashing this great keynote by Margaret McFall-Ngai 🤩

I ended up asking for advice from her biogeography work from 1 mm 🦑 to 3 microns 🦠 to 0.5 micron (reflectin protein) resolutions for #SpatialTranscriptomics as we go from 100 to 2 microns with Visium to #VisiumHD

Check this journal club presentation by @nick-eagles.bsky.social on:

> #ENACT: End-to-End Analysis of Visium High Definition (HD) Data

Nick also compared #ENACT against #bin2cell

#VisiumHD @10xgenomics.bsky.social #PyStats

📼 youtu.be/0D6l01ArI9M

Screenshot showing Nick Eagles' Visium HD overview slide that illustrates the 2 micron, 8 micron, and 16 micron bin level resolutions. An eukaryotic cell will typically overlap more than one bin.

Last Thursday @nick-eagles.bsky.social presented preliminary exploration results on how to analyze #VisiumHD with open-source software (mostly #RStats & #PyStats)

Some of it was designed for #VisiumHD, but some was preexisting

We are excited about this new #SpatialTranscriptomics frontier! 🌌 🔭

🆕 journal club by Nick Eagles:

#Bin2cell reconstructs cells from high resolution #VisiumHD data

by Polański #RBartolom et al from #teichlab #YayonNadav labs

📜 doi.org/10.1093/bioi...
🛝 speakerdeck.com/nickeagles/e...
📽️ youtu.be/ZY9N4spEZ_Q

#SpatialTranscriptomics

Bin2cell reconstructs cells from high resolution #VisiumHD data

Transforming #VisiumHD 2-μm matrix into Single-Cell Spatial data

StarDist segmentation for nuclei detection

#Bioinformatics 2024
academic.oup.com/bioinformati...

#VisiumHD #SpatialTranscriptomics #ColorectalCancer
FFPE sections
Continuous 2-µm matrix

2-µm bins assigned to nuclei polygon-> gene by nuclei UMI matrix-> map rare single cells in & around tumors

#10xGenomics bioRxiv 2024
www.biorxiv.org/content/10.1...