#Stereo-seq
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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
wiringthebrain.bsky.social
Single-cell spatial transcriptomic atlas of the whole mouse brain 🐭🧠 www.cell.com/neuron/fullt... - incredible resource! At both adult and developing stages! 👏
Single-cell spatial transcriptomic atlas of the whole mouse brain
Han et al. used snRNA-seq and Stereo-seq to generate a detailed mouse brain atlas with over 4 million spatially resolved cells and 29,655 genes. Their findings include region- enriched cell clusters a...
www.cell.com
July 18, 2025 at 5:53 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
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
pgj.bsky.social
#BondSoundsTOP25
#MusicChallenge

24: 'Mr. Kiss, Kiss, Bang, Bang' - Shirley Bassey

The theme tune we should have had for 'Thunderball'.

youtu.be/l1debbldqGc?...
Thunderball - alternate title seq. - Shirley Bassey - HD STEREO
YouTube video by The xNYr
youtu.be
September 11, 2025 at 8:49 PM
labwaggoner.bsky.social
Stereo-seq V2 facilitates single-cell-resolution spatial RNA mapping in FFPE samples through random primer capture, uncovering ncRNAs, host-pathogen transcriptome profiling, and spatial immune repertoires in situ @cellcellpress.bsky.social
www.cell.com/cell/fulltex...
August 28, 2025 at 10:08 PM
4130chromo.bsky.social
Stereo-seq V2: Spatial mapping of total RNA on FFPE sections with high resolution www.cell.com/cell/fulltex...
Stereo-seq V2: Spatial mapping of total RNA on FFPE sections with high resolution
Stereo-seq V2 facilitates single-cell-resolution spatial RNA mapping in FFPE samples through random primer capture, uncovering ncRNAs, host-pathogen transcriptome profiling, and spatial immune reperto...
www.cell.com
September 8, 2025 at 7:56 PM
haoyin.bsky.social
Systematic comparison of 11 sequencing-based #SpatialTranscriptomics methods 🤠
Visium
DynaSpatial
HDST
BMKMANU S1000
Slide-seq V2
Curio Seeker
Slide-tag
Stereo-seq
PIXEL-seq
Salus
DBiT-seq
Guess which behaves best for🧠microvasculature?😁

#naturemethods 2024
www.nature.com/articles/s41...
July 6, 2024 at 11:05 AM
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
haoyin.bsky.social
STORIES
SpatioTemporal Omics eneRgIES

Learning Waddington epigenetic (+regulon) landscape from multi-time-point Stereo-seq #SpatialTranscriptomics

Fused Gromov-Wasserstein #OptimalTransport
Linear▶️gene expression error
Quadratic▶️spatial consistency

bioRxiv 2025
www.biorxiv.org/content/10.1...
July 6, 2025 at 11:28 AM
haoyin.bsky.social
#SpatialTranscriptomics Stereo-seq 👤Carotid #Atherosclerosis

IntraPlaque #TertiaryLymphoidOrgan😎
CD138+ Plasma cells +diverse B cells

❎ #GerminalCenter
✅ #Lymphangiogenesis ✅#HEV
Col5A1+ fibroblast-like #SmoothMuscleCell as #LymphoidTissueOrganizer

#NatCVR 2025
www.nature.com/articles/s44...
April 30, 2025 at 11:34 AM
haoyin.bsky.social
Systematic comparisons among 4 subcellular-resolution #SpatialTranscriptomics methods

Stereo-seq v1.3
Visium HD FFPE
CosMx 6k
Xenium 5k

Human Tumors
Ground truth CODEX, +scRNAseq

#NatComm 2025
www.nature.com/articles/s41...
October 24, 2025 at 10:45 AM
lpjlab.org
A super cool #single-cell spatial transcriptomic mouse #brain atlas is out! 🐭🧠🔬
Unveiling cell types, #gene expression, & TF dynamics across the whole brain!
Awesome! ✨
#neuroskyence #neuroscience #compneurosky

www.cell.com/neuron/fullt...
Single-cell spatial transcriptomic atlas of the whole mouse brain
Han et al. used snRNA-seq and Stereo-seq to generate a detailed mouse brain atlas with over 4 million spatially resolved cells and 29,655 genes. Their findings include region- enriched cell clusters a...
www.cell.com
July 9, 2025 at 7:11 PM
plosbiology.org
The #PrefrontalCortex is key for higher cognitive functions, but how do its circuits mature? This study provides a #transcriptomic resource for the mouse #PFC over 84 days of development, revealing cell population dynamics & expression of #psychiatric risk genes
@plosbiology.org 🧪 plos.io/45bhRLU
Spatiotemporal molecular and cellular atlas of mouse PFC during postnatal development. Top left: UMAP of all cells in mouse PFC from scRNA-seq data, colored by cell subtypes. Im, immature. Top right: UMAP of all cells in mouse PFC from scRNA-seq data, colored by time stages. Bottom left: Spatial distribution of all cell subtypes in mouse PFC from P1 stereo-seq data. Bottom right: Spatial distribution of all cell subtypes in mouse PFC from adult stereo-seq data.
January 13, 2026 at 5:35 PM
plosbiology.org
The #PrefrontalCortex is key for higher cognitive functions, but how do its circuits mature? This study provides a #transcriptomic resource for the mouse #PFC over 84 days of development, revealing cell population dynamics & expression of #psychiatric risk genes @plosbiology.org 🧪 plos.io/45bhRLU
Spatiotemporal molecular and cellular atlas of mouse PFC during postnatal development. Top left: UMAP of all cells in mouse PFC from scRNA-seq data, colored by cell subtypes. Im, immature. Top right: UMAP of all cells in mouse PFC from scRNA-seq data, colored by time stages. Bottom left: Spatial distribution of all cell subtypes in mouse PFC from P1 stereo-seq data. Bottom right: Spatial distribution of all cell subtypes in mouse PFC from adult stereo-seq data.
January 13, 2026 at 10:22 AM
cp-cell.bsky.social
Now online! Stereo-seq V2: Spatial mapping of total RNA on FFPE sections with high resolution
Stereo-seq V2: Spatial mapping of total RNA on FFPE sections with high resolution
Stereo-seq V2 facilitates single-cell-resolution spatial RNA mapping in FFPE samples through random primer capture, uncovering ncRNAs, host-pathogen transcriptome profiling, and spatial immune repertoires in situ.
dlvr.it
August 29, 2025 at 12:41 PM
lcolladotor.bsky.social
Lei Li @leili-bioinfo.bsky.social will now talk about high resolution spatial with #Stereo-seq

#SpatialBiology
December 5, 2024 at 5:23 PM
haoyin.bsky.social
PASTE2

Partial alignment (based on a subset of spots) of multi-slice #SpatialTranscriptomics

3D reconstruction of 16-slide Stereo-seq Drosophila embryo

Partial fused Gromov-Wasserstein #OptimalTransport

vs PASTE Pamona Tangram

#GenomeRes 2023
genome.cshlp.org/content/33/7...
March 22, 2025 at 11:11 AM
wukang.bsky.social
With these enhancements, Stereo-seq V2 can perform mapping of total RNAs on FFPE sections with high resolution.
August 31, 2025 at 1:19 AM
mictott.bsky.social
Full-length single-cell spatial transcriptomics reveals spatial and cell-type-specific transcript isoforms in the primate brain www.nature.com/articles/s41...
Full-length single-cell spatial transcriptomics reveals spatial and cell-type-specific transcript isoforms in the primate brain - Nature Methods
Fullscope-seq combines a spatial transcriptomics approach (Stereo-seq) with long-read sequencing. The approach provides isoform information at single-cell resolution across a large field of view, as d...
www.nature.com
July 30, 2026 at 1:12 PM
shihcheng.bsky.social
Gene expression insights from 77 sections of 13 human embryos (Carnegie stages 12-23) using Stereo-seq and snRNA-seq pave the way for understanding development. PMID:42203883, Nature 2026, @Nature https://doi.org/10.1038/s41586-026-10545-0 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪
Spatiotemporal transcriptome atlas of human embryos after gastrulation | Nature
The comprehensive spatiotemporal atlas of gene expression during early human embryonic development is critical for insights into embryogenesis1, organogenesis2 and disease origins3,4. Here, leveraging Stereo-seq technology, we generated spatial transcriptomic profiles across 77 sagittal sections of 13 whole-human embryos ranging from Carnegie stage 12 to 23, integrated with single-nucleus RNA sequencing to elucidate gene expression patterns within defined cellular contexts, revealing the cellular heterogeneity that drives organ-specific differentiation. Our study has established a regulatory profile for the development of 50 organs and 198 substructures, and identified potential tissue-identity regulators. Of note, it uncovered previously uncharacterized gene functions in cardiac and brain development. The atlas not only substantiates and refines the current understanding of human organ development but also highlights key organs susceptible to genetic disorders. Furthermore, we charact
doi.org
June 29, 2026 at 10:00 AM
ihgatucsf.bsky.social
Join @completegenomics.bsky.social for a focused lunch & learn seminar on Stereo-seq
humangenetics.ucsf.edu/ucsf-ihg-cat...
August 27, 2025 at 8:19 PM
yuminzheng.bsky.social
(1/n) Excited to share our new work accepted at ICML 2025. SUICA, a novel method to enhance the quality of spatial transcriptomics from multiple ST platforms including Visium, stereo-seq, slide-seq-V2....
#SpatialTranscriptomics
Paper at: arxiv.org/abs/2412.01124
Code at: github.com/Szym29/SUICA
SUICA pipeline
May 19, 2025 at 4:31 PM
mariosgeorgakis.bsky.social
A very nice paper applying spatial single-cell transcriptomics (Stereo-seq) to human carotid plaques❗️

It identifies tertiary lymphoid organs within plaques and links them to symptomatic cerebrovascular disease (stroke/TIA) 🧠
May 3, 2025 at 4:56 PM
plosbiology.org
The #PrefrontalCortex is key for higher cognitive functions, but how do its circuits mature? This study provides a #transcriptomic resource for the mouse #PFC over 84 days of development, revealing cell population dynamics & expression of #psychiatric risk genes
@plosbiology.org 🧪 plos.io/45bhRLU
Spatiotemporal molecular and cellular atlas of mouse PFC during postnatal development. Top left: UMAP of all cells in mouse PFC from scRNA-seq data, colored by cell subtypes. Im, immature. Top right: UMAP of all cells in mouse PFC from scRNA-seq data, colored by time stages. Bottom left: Spatial distribution of all cell subtypes in mouse PFC from P1 stereo-seq data. Bottom right: Spatial distribution of all cell subtypes in mouse PFC from adult stereo-seq data.
January 13, 2026 at 2:05 PM