#Spatialtranscriptomics
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tkcaccia.bsky.social
KODAMA goes spatial.
doi.org/10.1101/2025...
#spatialtranscriptomics #visium #visiumhd #seurat #giotto
June 2, 2025 at 8:22 PM
haoyin.bsky.social
TRISCO

A solid step closer to 3D #SpatialTranscriptomics 😎

Optimized probe-based 3D RNA imaging in whole organs

isHCR
Tris 500 mM
4'C
Validated probe list in Table S1
Brain Heart Lung Kidney

@peruhlen.bsky.social @science.org 2024
www.science.org/doi/10.1126/...
November 26, 2024 at 1:10 PM
pmarignani.bsky.social
Anyone interested in #singlecell and #spatialtranscriptomics, join our conversation. go.bsky.app/UfPCLPW
November 16, 2024 at 8:49 PM
halloulab.bsky.social
🚨3-year Postdoc Position @halloulab.bsky.social (Kennedy Institute, Oxford) - on Spatial Biology & Bioinformatics of Fibrosis🚨

An exciting project combining #SpatialTranscriptomics & #Mechanobiology👇:

shorturl.at/LLS5r

Deadline: 16 March - Please RT 📢!

@kiroxford.bsky.social @ox.ac.uk
March 2, 2026 at 7:58 AM
haoyin.bsky.social
#SpatialTranscriptomics

STcompare
github.com/JEFworks-Lab...

Test your gene of interest if it is differentially spatially patterned (r, p, s)🤠
Spatial correlation
Spatial fold change
Control for spatial autocorrelation

@jef.works bioRxiv 2025
www.biorxiv.org/content/10.1...
December 12, 2025 at 12:43 PM
yahayayabo.bsky.social
Amazing talk by
Henrik Heiland
on using #spatialtranscriptomics data to model glioblastoma evolution #SNO2024
November 22, 2024 at 10:14 PM
haoyin.bsky.social
Comparative analysis of commercial Imaging-based #SpatialTranscriptomics methods

Xenium
CosMx 1k
MERSCOPE

Tissue Microarray
17 tumor+16 normal tissue

Transcript count
vs Reference RNAseq
Segmentation accuracy
Cell type annotation

#NatComms 2025
www.nature.com/articles/s41...
December 1, 2025 at 12:52 PM
jef.works
Check out our updated scatterbar package for visualizing proportional data across spatial coordinates like deconvolved cell types in #spatialtranscriptomics using stacked bar plots (alternative to scatterpies)!

Preprint: www.biorxiv.org/content/10.1...
Code: github.com/JEFworks-Lab...

#dataviz
November 22, 2024 at 2:57 PM
sawitzkilab.bsky.social
Waking up our sleeping beauty!
Super excited to have Xenium and PhenoCycler now running in the same room 🤩

#SpatialOmics #SpatialBiology #SpatialProteomics #SpatialTranscriptomics #Immunology
April 3, 2025 at 9:05 AM
haoyin.bsky.social
Myocilin marks the glia limitans superficialis Astrocyte

Re-analysis of brain-wide #SpatialTranscriptomics & sc-/sn-RNAseq data➡️
Myoc+ 2% of total astrocytes covering brain/spinal cord surface

@philiphasel.bsky.social
@liddelowsa.bsky.social
#CellRep 2025
www.cell.com/cell-reports...
July 12, 2025 at 7:00 PM
haoyin.bsky.social
Comparing single-cell #SpatialTranscriptomics methods on FFPE human tumor #TissueMicroArray

CosMx 1k vs MERFISH 500 vs Xenium-UM/-MM 339
93 common genes

lung adenocarcinoma
pleural mesothelioma

Corr. Bulk RNAseq, GeoMx

#NatureComms 2025
www.nature.com/articles/s41...
September 28, 2025 at 12:22 PM
haoyin.bsky.social
#SpatialTranscriptomics #Atherosclerosis

A first CosMx 1k plex single-cell map of👤coronary atherosclerosis😆

From Adaptive intimal thickening to Large Atheromatous plaque with intralesional fibrosis

bioRxiv 2025
www.biorxiv.org/content/10.1...
April 6, 2025 at 11:16 AM
haoyin.bsky.social
RAEFISH
Reverse-padlock Amplicon Encoding FISH

Genome-wide Imaging-based #SpatialTranscriptomics
>16k coding RNA + >5k LncRNA
>500 genes/cell detected on frozen sections of🐭liver/placenta

Spatial gRNA seq➡️imaging-based CRISPR screening in vitro😎

bioRxiv 2025
www.biorxiv.org/content/10.1...
March 23, 2025 at 11:55 AM
albyxhsu.bsky.social
New platform, new data ! @spatialtranscriptomics @SpatialBiologySummit
February 7, 2024 at 4:27 AM
earlhaminst.bsky.social
Registration closes this coming Monday 29 June! 👇

#singlecell #spatial #spatialtranscriptomics
earlhaminst.bsky.social Earlham Institute @earlhaminst.bsky.social · May 25
Be part of a supportive and engaged community of #singlecell and #spatial scientists! 🧬💻🔎

Register for the Norwich Single-Cell and Spatial Symposium and discover the latest methods across diverse living systems. 🌱🧠🐟️

Take a look at our full programme: buff.ly/2KvQ3Zv

#EISingleCell26
Speaker profile of Tatsuya Nobori from The Sainsbury Lab. Talk title: Dissecting plant-microbe interactions with single-cell and spatial omics technologies. Speaker profile of Ava Khamseh from the Institute of Cancer & Genetics in Edinburgh. Talk title: Single-cell (sub)type and state quantification at high resolution with uncertainty quantification Speaker profile of Ang Li from the University of Oxford. Talk title: Methods of integrating GWAS and single-cell data Speaker profile of Alina Kurjan, from University of Oxford and Entelo Bio. Talk title: When tendon grows up: cellular divergence from development to adult life.
June 26, 2026 at 9:42 AM
haoyin.bsky.social
#SpatialTranscriptomics #Atherosclerosis

Mapping the Senescence (SenMayo CellAge) in p16 reporter🐭aortic atherosclerotic lesions
scRNAseq GeoMx
🔥 #SmoothMuscleCell Fibroblast T

#Senolytic ABT-737 ⏫plaque collagen fibers ⏬necrotic core ⏬serum cytokines

#NatAging 2025
www.nature.com/articles/s43...
July 15, 2025 at 7:17 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
3D #SpatialTranscriptomics #Zebrafish🐟 #Gut #EntericNervousSystem 4~7 dpf 😍
12-gene multiplex whole-mount #HybridizationChainReaction
Cell proximity network

@rodrigomorec.bsky.social @uribelab.bsky.social bioRxiv 2025
www.biorxiv.org/content/10.1...
April 22, 2025 at 7:22 PM
jef.works
By shedding light on off-target probe binding + providing a tool to enable prediction, we hope this work will enhance the quality of #spatialtranscriptomics data + improve reproducibility in #spatialtranscriptomics research (13/13)

🎉 Team Caleb Hallinan, Hayden Ji, and @stevensalzberg.bsky.social
April 3, 2025 at 3:55 PM
haoyin.bsky.social
#SpatialTranscriptomics #CellSegmentation

FastReseg
github.com/Nanostring-B...

Using transcript scoring +"spatial doublet" test to rectify segmentation errors🥸

vs transcript-dominant approaches: Baysor Proseg

#SciReports 2025
www.nature.com/articles/s41...
March 22, 2026 at 1:02 PM
haoyin.bsky.social
#SpatialRNAEncyclopedia
Patho-DBiT
#SpatialTranscriptomics FFPE

Spatial Co-mapping of RNA Expression Splicing Editing SNV AND ncRNAs (miRNA lncRNA rRNA snRNA)👹

in situ polyA tailing

10 μm/px➡️ >2000 genes Lymphoma

@rongfan8.bsky.social @cellcellpress.bsky.social 2025
www.cell.com/cell/fulltex...
February 24, 2025 at 12:49 PM
haoyin.bsky.social
#SpatialTranscriptomics

There are 11 methods (CNN- or Transformer-based) enabling predicting spatial gene expression from H&E histology😆

Which behaves?
DeepPT
EGNv1 EGNv2
Hist2ST
THItoGene
DeepSpaCE
TCGN
ST-Net
iStar
HisToGene
GeneCodeR

@naturecomms.bsky.social 2025
www.nature.com/articles/s41...
February 16, 2025 at 12:33 PM
jsantoyo.bsky.social
Cell-type deconvolution methods for spatial transcriptomics. #SpatialTranscriptomics #CellTypeDeconvolution #Bioinformatics #Genomics @natrevgenet.nature.com 🧬 🖥️
www.nature.com/articles/s41...
July 4, 2025 at 8:31 AM
loicaroyer.bsky.social
🧬🔬🧪 We are seeking a Scientist to push the limits of spatial transcriptomics in zebrafish! Come join us!
#MolBio #SpatialTranscriptomics #DevelopmentalBiology #ScienceJobs 🧫🐟🔍

job-boards.greenhouse.io/chanzuckerbe...
Scientist, Spatial Molecular Cartography (Jacobo/Royer Group - Biohub SF)
San Francisco, California, United States
job-boards.greenhouse.io
April 15, 2025 at 6:27 PM
haoyin.bsky.social
Robust decomposition of cell type mixtures in sequencing-based #SpatialTranscriptomics
RCTD

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

Cell type-specific inference of differential expression in spatial transcriptomics
C-SIDE

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

spacexr
github.com/dmcable/spac...
July 30, 2026 at 1:32 PM