KODAMA goes spatial.
doi.org/10.1101/2025...
#spatialtranscriptomics #visium #visiumhd #seurat #giotto
doi.org/10.1101/2025...
#spatialtranscriptomics #visium #visiumhd #seurat #giotto
June 2, 2025 at 8:22 PM
KODAMA goes spatial.
doi.org/10.1101/2025...
#spatialtranscriptomics #visium #visiumhd #seurat #giotto
doi.org/10.1101/2025...
#spatialtranscriptomics #visium #visiumhd #seurat #giotto
#visiumhd product updates : segmentation , visium HD XL , visium hd 3’ @10xgenomics.bsky.social #agbt25
February 23, 2025 at 8:10 PM
#visiumhd product updates : segmentation , visium HD XL , visium hd 3’ @10xgenomics.bsky.social #agbt25
Hey #ACNP2024 - Michael Totty, postdoc w/ our group is presenting some super awesome spatial transcriptomics of human amygdala 🧠 today in the Data Blitz session (11:30-1). Data includes Visium across extent of the structure PLUS cellular resolution Xenium and some really new VisiumHD!
December 8, 2024 at 5:13 PM
Hey #ACNP2024 - Michael Totty, postdoc w/ our group is presenting some super awesome spatial transcriptomics of human amygdala 🧠 today in the Data Blitz session (11:30-1). Data includes Visium across extent of the structure PLUS cellular resolution Xenium and some really new VisiumHD!
The unique expression profile, topography, and distribution of D1-islands lead us to use VisiumHD to gain a better understanding of their transcriptional heterogeneity. We found that D1_Island_A consists of two distinct populations of D1-MSNs that exhibit high expression of OPRM1, TSHZ1, and RXFP1.
September 27, 2026 at 5:10 PM
The unique expression profile, topography, and distribution of D1-islands lead us to use VisiumHD to gain a better understanding of their transcriptional heterogeneity. We found that D1_Island_A consists of two distinct populations of D1-MSNs that exhibit high expression of OPRM1, TSHZ1, and RXFP1.
Wanted to learn more about VisiumHD barcodes to help build better tools for processing that exciting data
I asked 10x about parsing the binary spatial information file, they said:
"...the Visium HD barcodes...are proprietary..."
C'mon 10x. You're shooting yourselves (and users) in the foot here!
I asked 10x about parsing the binary spatial information file, they said:
"...the Visium HD barcodes...are proprietary..."
C'mon 10x. You're shooting yourselves (and users) in the foot here!
November 26, 2024 at 12:29 AM
Wanted to learn more about VisiumHD barcodes to help build better tools for processing that exciting data
I asked 10x about parsing the binary spatial information file, they said:
"...the Visium HD barcodes...are proprietary..."
C'mon 10x. You're shooting yourselves (and users) in the foot here!
I asked 10x about parsing the binary spatial information file, they said:
"...the Visium HD barcodes...are proprietary..."
C'mon 10x. You're shooting yourselves (and users) in the foot here!
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.
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.
VisiumHD: From 16 µm to 2 µm resolution — sainsc 0.2.2.dev5+g0c33c57 documentation
sainsc.readthedocs.io
November 29, 2024 at 10:32 AM
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.
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.
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/...
speakerdeck.com/lcolladotor/...
SpatialBiologyWestCoastUS2024
speakerdeck.com
December 5, 2024 at 3:17 PM
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/...
speakerdeck.com/lcolladotor/...
Recordings are now available for the Spatial Omics workshop focused on VisiumHD by @10xgenomics.bsky.social
Access the recordings here: youtube.com/playlist?lis...
Access the recordings here: youtube.com/playlist?lis...
The Princess Margaret Genomics Centre’s (PMGC) Brain Single Cell Initiative collaborated with Panoramics-A Vision and Bioinformatics.ca to host a two-day hybrid spatial-omics workshop packed with avid researchers from across Canada.
Please visit our website: www.pmgenomics.ca/pmgenomics/.
Please visit our website: www.pmgenomics.ca/pmgenomics/.
April 23, 2025 at 2:01 PM
Recordings are now available for the Spatial Omics workshop focused on VisiumHD by @10xgenomics.bsky.social
Access the recordings here: youtube.com/playlist?lis...
Access the recordings here: youtube.com/playlist?lis...
In this #codetutorial blog post, I demonstrate a multi-sample integrative #dataanalysis of VisiumHD #spatialtranscriptomics data using geometric sketching with Harmony in Seurat to identify transcriptionally similar tissue structures.
Try it out for yourself: jef.works/blog/2025/04...
#AcademicSky
Try it out for yourself: jef.works/blog/2025/04...
#AcademicSky
April 23, 2025 at 2:33 PM
In this #codetutorial blog post, I demonstrate a multi-sample integrative #dataanalysis of VisiumHD #spatialtranscriptomics data using geometric sketching with Harmony in Seurat to identify transcriptionally similar tissue structures.
Try it out for yourself: jef.works/blog/2025/04...
#AcademicSky
Try it out for yourself: jef.works/blog/2025/04...
#AcademicSky
Mateusz Garbulowski et al used custom #VisiumHD to study spatial host-microbiome (SHM-seq) interactions
They also built #homic on top of #Kraken2 for accurate taxonomic classification of SHM-seq data
QR code was deactivated, but go to github.com/mategarb/homic
#BoG2026 @cshlmeetings.bsky.social
They also built #homic on top of #Kraken2 for accurate taxonomic classification of SHM-seq data
QR code was deactivated, but go to github.com/mategarb/homic
#BoG2026 @cshlmeetings.bsky.social
May 7, 2026 at 3:48 PM
Mateusz Garbulowski et al used custom #VisiumHD to study spatial host-microbiome (SHM-seq) interactions
They also built #homic on top of #Kraken2 for accurate taxonomic classification of SHM-seq data
QR code was deactivated, but go to github.com/mategarb/homic
#BoG2026 @cshlmeetings.bsky.social
They also built #homic on top of #Kraken2 for accurate taxonomic classification of SHM-seq data
QR code was deactivated, but go to github.com/mategarb/homic
#BoG2026 @cshlmeetings.bsky.social
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
May 20, 2025 at 9:20 PM
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
May 13, 2025 at 4:01 PM
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
Happy to share our new preprint: Subcellular mRNA localization patterns across tissues resolved with spatial transcriptomics: www.biorxiv.org/content/10.1...
We utilize VisiumHD to extract intra-cellular mRNA polarization patterns in epithelial tissues.
We utilize VisiumHD to extract intra-cellular mRNA polarization patterns in epithelial tissues.
September 10, 2025 at 11:14 AM
Happy to share our new preprint: Subcellular mRNA localization patterns across tissues resolved with spatial transcriptomics: www.biorxiv.org/content/10.1...
We utilize VisiumHD to extract intra-cellular mRNA polarization patterns in epithelial tissues.
We utilize VisiumHD to extract intra-cellular mRNA polarization patterns in epithelial tissues.
We next barcoded mesoderm and analyzed heart development with single cell lineage tracing and VisiumHD to again annotate all the new cell types with high confidence.
September 23, 2026 at 5:00 PM
We next barcoded mesoderm and analyzed heart development with single cell lineage tracing and VisiumHD to again annotate all the new cell types with high confidence.
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! 🧬🧠💻
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! 🧬🧠💻
February 24, 2025 at 1:35 PM
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! 🧬🧠💻
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! 🧬🧠💻
So we barcoded mesoderm at E7.5, and analyzed liver development at E16.5 with single cell lineage tracing and VisiumHD to annotate the many new cell types/states in a spatially aware manner, with high confidence.
September 23, 2026 at 5:00 PM
So we barcoded mesoderm at E7.5, and analyzed liver development at E16.5 with single cell lineage tracing and VisiumHD to annotate the many new cell types/states in a spatially aware manner, with high confidence.
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
June 12, 2025 at 7:25 AM
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
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! 🌌 🔭
Some of it was designed for #VisiumHD, but some was preexisting
We are excited about this new #SpatialTranscriptomics frontier! 🌌 🔭
November 19, 2024 at 6:55 PM
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! 🌌 🔭
Some of it was designed for #VisiumHD, but some was preexisting
We are excited about this new #SpatialTranscriptomics frontier! 🌌 🔭
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
June 11, 2025 at 4:00 PM
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
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
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
May 8, 2025 at 4:23 AM
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
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
#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?...
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?...
June 10, 2025 at 2:48 PM
#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?...
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?...
We next chose to use VisiumHD to provide full-transcriptome profiling at single cell resolution to characterize the intercalated cells and central nucleus. Combing this with reference atlases revealed at least 3 reproducible ITC cell types - two island and one non-island population. 8/12
August 27, 2026 at 12:14 PM
We next chose to use VisiumHD to provide full-transcriptome profiling at single cell resolution to characterize the intercalated cells and central nucleus. Combing this with reference atlases revealed at least 3 reproducible ITC cell types - two island and one non-island population. 8/12
📢 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
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
September 4, 2025 at 2:25 AM
📢 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
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
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!
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 ...
www.nature.com
January 16, 2025 at 12:36 AM