#Visium
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lcolladotor.bsky.social
I'm thrilled to share with you that #visiumStitched led by @nick-eagles.bsky.social has now been published

Our #RStats / @bioconductor.bsky.social 📦 provides a framework for stitching together multiple #Visium @10xgenomics.bsky.social capture areas together

#AcademicSky

doi.org/10.1186/s128...
November 18, 2024 at 4:32 PM
catharineaquino.bsky.social
#visiumhd product updates : segmentation , visium HD XL , visium hd 3’ @10xgenomics.bsky.social #agbt25
February 23, 2025 at 8:10 PM
dcapto.bsky.social
Continually astounded with all that is now known about the debilitating health “issue” that won’t be named, that not even high-paid athletes are being protected—valuable assets to team owners who should want to protect their investment. Except for the Miami Dolphins organization, they know what’s up
July 9, 2026 at 2:07 AM
tkcaccia.bsky.social
KODAMA goes spatial.
doi.org/10.1101/2025...
#spatialtranscriptomics #visium #visiumhd #seurat #giotto
June 2, 2025 at 8:22 PM
lpachter.bsky.social
Another example of the different results one gets from a Scanpy vs. Seurat analysis, in this case a Visium HD dataset from academic.oup.com/bioinformati...
13 vs. 20 clusters. And qualitatively different results, corroborating what we saw in biorxiv.org/content/10.1...
November 25, 2024 at 6:10 PM
haoyin.bsky.social
Riemannian Geometry, Optimal Transport & Spatial Multiomics Alignment 👹

Manifold Gromov-Wasserstein vs moscot SCOTv2 SpatialMeta

Visium + Xenium
Visium + #MassSpecImaging spatial metabolomics

Admit I have0️⃣understanding of the mathematical machinery😅

bioRxiv 2025
www.biorxiv.org/content/10.6...
March 24, 2026 at 7:09 PM
alforrest.bsky.social
Wow head-to-head comparison Visium HD FFPE, CosMx 6K, Xenium 5K, Stereo-seq v1.3 and Visium HD FF profiling on HGSOC and HCC. Heads-up @GESTALT_sp hopefully can save community some $$$$
December 30, 2024 at 9:36 AM
moritzgerstung.bsky.social
This is a great set of methods for studying combinatorial effects of cancer mutations on spatial phenotypes.

Clever experimental design by @breinigmarco.bsky.social hijacking Visium and elegant analysis by @lomakinai.bsky.social and @elihei.bsky.social

www.nature.com/articles/s41...
Integrated in vivo combinatorial functional genomics and spatial transcriptomics of tumours to decode genotype-to-phenotype relationships - Nature Biomedical Engineering
A method integrates perturbation mapping with 10X Visium spatial transcriptomics to map tumour genetic complexity and heterogeneity.
www.nature.com
July 29, 2025 at 5:51 AM
panaccindex.bsky.social
The Biden Administration diverted pandemic relief funding to cops so they can better terrorize our communities instead of deploying technology that can actually protect Americans from SARS-CoV-2 transmission. visium.one/case-studies...
Miami Dolphins - Visium
Explore the case study of Visium Far-UVC light fixtures installed at the Miami Dolphins training facility.
visium.one
July 5, 2026 at 1:38 AM
stephenturner.us
scatterbar: an R package for visualizing proportional data across spatially resolved coordinates www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/JEFworks-Lab...
Nice #Rstats pkg from @jef.works. Vignettes for SpatialExperiment + Visium scRNA-seq data
May 20, 2025 at 8:02 PM
albertvilella.bsky.social
What is @10xgenomics.bsky.social announcing at AGBT? My bet is for Visium HD poly-A for non-Human/Mouse fresh frozen samples.
10xgenomics.bsky.social 10x Genomics @10xgenomics.bsky.social · Feb 13
10x Genomics is excited to be back for AGBT 2025. Don’t miss our pre-conference workshop: Sunday, Feb. 23 from 1–4 PM ET. Can’t make it? Have no fear. Register for our livestream and you won’t miss a beat: bit.ly/4gB5z2g
February 13, 2025 at 8:32 PM
haoyin.bsky.social
#SpatialTranscriptomics #BatchCorrelation

SpaBatch

Align multi-slice sequencing-based spatial data
Visium ST Stereo-seq

#VariationalGraphAutoEncoder
Masked data augmentation

vs STG3Net STAligner SEDR DeepST SpaGIC STitch3D

bioRxiv 2025
www.biorxiv.org/content/10.1...
May 22, 2025 at 12:22 PM
haoyin.bsky.social
GASTON
Gradient Analysis of #Spatialtranscriptomics Organization with Neural networks

"models gene expression as a Piecewise linear function of the Isodepth"

Work with Visium Xenium MERFISH Slide-seq V2 Stereo-seq

@uthsav.bsky.social @naturemethods.bsky.social 2025
www.nature.com/articles/s41...
March 6, 2025 at 12:23 PM
albertvilella.bsky.social
www.nature.com/articles/s41... Spatial Biology peer reviewed paper comparing BGI Stereo-Seq to Brulee Spatial to @10xgenomics.bsky.social Visium/Xenium
October 23, 2025 at 2:20 AM
rgottardo.bsky.social
🎉 New paper alert. We benchmarked Visium, GeoMx, and Chromium for FFPE tumor analysis. Thanks @estellayixingdong.bsky.social for pushing this forward, & MOSAIC collaborators!
📄 www.nature.com/articles/s41...
#SpatialTranscriptomics #CancerResearch cc: @owkin.bsky.social @10xgenomics.bsky.social
Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity - Nature Communications
Currently, there is an urgent need to evaluate the strengths and limitations of various probe-based full transcriptome methods for formalin-fixed paraffin-embedded tumor tissues. Here, the authors ana...
www.nature.com
June 22, 2025 at 6:20 AM
rphillips3.bsky.social
First #FluorescenceFriday post! Some islands in the human NAc 🏝️🧠. Forever fascinated with this really cool population. Shoutout to @svitlanabach.bsky.social for the incredible Visium-HD targeting!
March 20, 2026 at 6:21 PM
martinowk.bsky.social
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
gregorylab.bskyverified.social
Interested in joining our team? Please apply!!

##Bioinformatics #SpatialTranscriptomics #Xenium #Visium #PostDoc #Hiring #MolecularBiology #Genomics #scRNAseq #Neuroscience 🧬💻🧠
gregorylab.bskyverified.social The Gregory Lab @ DukeU @gregorylab.bskyverified.social · Dec 17
Seeking #PostDoc to join the Gregory lab in the #BrainTumorOmics Program, performing cutting-edge #singlecell and #spatialtranscriptomics techniques & studying mechanisms driving development & progression of #glioma 🧠

shttps://careers.duke.edu/job/Durham-POSTDOCTORAL-ASSOCIATE-NC-27710/1243119300/
POSTDOCTORAL ASSOCIATE
POSTDOCTORAL ASSOCIATE
careers.duke.edu
January 3, 2025 at 2:41 PM
haoyin.bsky.social
Glomerular Neovascularization
#DiabeticKidneyDisease #CaseReport

#SpatialTranscriptomics #Visium @10xGenomics

50-μm section multiplex IF

TEM▶️⏫Periglomerular Capillaries + de novo vascular anastomosis crossing Bowmen capsule

#KPMProject #CJASN 2024
journals.lww.com/cjasn/abstra...
February 5, 2025 at 12:49 PM
deniswirtz.bsky.social
The CODA workflow works for:
- any tissue type (eye, kidney, pancreas, brain,...)
- any disease (cancer, fibrosis, diabetes,...)
- any species (human, mouse, rhesus macaque, ...)

It can be integrated with any spatial omic technique (CODEX, Visium, IF, IHC,..)

www.nature.com/articles/s41...
April 19, 2026 at 2:39 PM
haoyin.bsky.social
#SpatialOmics

STAnalyzer
Human-in-the-Loop Multi-agent (Orchestrator/Service Planner/Data Interpretation/Knowledge Integration) framework

www.sdu-idea.cn/STAnalyzer/

Work on Visium Xenium

From raw counts to hypothesis generation

bioRxiv 2026
www.biorxiv.org/content/10.6...
April 19, 2026 at 11:12 AM
haoyin.bsky.social
#SpatialTranscriptomics #Visium @10xGenomics #AbdominalAorticAneurysm

THBS1/Thrombospodin-1 KO in Myeloid cell, not #EndothelialCell, ⬇️ #AorticAneurysm but⬆️ #AorticRupture in 🐭AAA AngII+Apoe KO

Likely compromised TGFb-ECM-stabilizing SMCs & fibroblasts

bioRxiv 2024
www.biorxiv.org/content/10.1...
December 25, 2024 at 11:53 AM
haoyin.bsky.social
#SpatialTranscriptomics #Visium #SlideSeq2
Human Kidney N>20
Healthy #AKI #CKD

Crazy loads of data to explore🤠

Does vascular niche affect the regenerative vs degenerative transition of adaptive epithelial states?🤓

#Nature 2024
www.nature.com/articles/s41...
February 1, 2025 at 1:16 PM
haoyin.bsky.social
#SpatialTranscriptomics #Visium #Xenium
Glomerular microvascular cell landscape shift in #DiabeticKidneyDisease

MEF2A/MEF2C/TRPS1 in Glomerular #EndothelialCell phenotypic plasticity & EC-to-Mural cell/Podocyte communications
SEMA6A-PLXNA2

bioRxiv 2024
www.biorxiv.org/content/10.1...
February 13, 2025 at 9:09 PM
scilife360.bsky.social
New Paper alert 🎉🎉🎉

Mild TBI results in extensive gene dysregulation!

#cellreports #neurotrauma #hippocampus #postdoc

@markcembrowski.bsky.social @briannabristow.bsky.social
Thrilled to share my latest paper published in Cell Reports - presenting findings on Gene expression dysregulation following mild Traumatic Brain Injury assessed by Visium spatial transcriptomics… | M...
Thrilled to share my latest paper published in Cell Reports - presenting findings on Gene expression dysregulation following mild Traumatic Brain Injury assessed by Visium spatial transcriptomics, mFI...
www.linkedin.com
June 13, 2025 at 7:06 AM