#Spatialtranscriptomics
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imm.ox.ac.uk
#WIMMReads

🧪 Can AI turn routine pathology images into molecular information?

A new review from Kexin Xu, Hashem Koohy and Agne Antanaviciute explores advances in predicting spatial gene expression directly from tissue images.

#SpatialTranscriptomics #DigitalPathology #MRCWIMM #AcademicSky
Predicting spatial transcriptomics from histology images: Progress, challenges, and directions
Spatial transcriptomics (ST) maps gene expression within intact tissues, but its cost and technical complexity limit broad adoption. A growing body of deep-learning methods now seeks to infer ST direc...
www.sciexplor.com
September 24, 2026 at 9:59 AM
exo-beyondthecell.bsky.social
New review in EXO - Beyond the Cell!
Title: Predicting spatial transcriptomics from histology images: Progress, challenges, and directions
Explore AI-powered virtual molecular profiling from H&E slides:
sciexplor.com/exo/articles...
#SpatialTranscriptomics #DigitalPathology #AI
September 24, 2026 at 2:29 AM
lingting-shi.bsky.social
Shoutout to co-first authors Ajna Uzuni and Ximi Wang, and to Michael Pressler
@michaelppressler.bsky.social
. Thanks also to the McFaline-Figueroa Lab
@jlmcfalinefigueroa.bsky.social
for their support. Check out our paper!
#GVHD #SingleCell #TCR #SpatialTranscriptomics #Immunology
September 17, 2026 at 6:15 PM
cancers-mdpi.bsky.social
🧬Spatial #Transcriptomics in #LungCancer and Pulmonary Diseases: A Comprehensive Review

🧑‍🔬by Da Hyun Kang, Yoonjoo Kim et al. from Chungnam National University

📊Cited 19 times!

Read it here🔗 www.mdpi.com/2072-6694/17...

#SpatialTranscriptomics #PulmonaryDisease #TumorMicroenvironment
Figure 4. Spatial transcriptomic signatures across pulmonary diseases: cellular niches and molecular pathways.
September 17, 2026 at 10:17 AM
gpbees.bsky.social
🧵 How can we reconstruct cellular spatial organization when spatial transcriptomics lacks single-cell resolution?

A new #GPB study introduces SPCC, a deep-learning framework integrating #scRNAseq and #SpatialTranscriptomics to infer spatial cell–cell interactions. 1/6
September 17, 2026 at 9:14 AM
onesinglecell.bsky.social
Our paper is out in Nature Methods! 🧑‍💻 There are 50+ methods for spatially-aware clustering on spatial transcriptomics data. How should we use them? A thread 🧵 (1/7)
📄 doi.org/10.1038/s415...
#spatialtranscriptomics #bioinformatics #computationalbiology
Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering - Nature Methods
Benchmarking spatially aware clustering is challenging. SACCELERATOR is an open-source, extensible framework that formalizes expert-guided spatial clustering analysis.
doi.org
September 13, 2026 at 10:11 AM
earlhaminst.bsky.social
📣 Save the date! The Norwich Single-Cell and Spatial Symposium returns in 2027.

Join a supportive forum for researchers working on similar challenges across diverse systems to discuss, network, and share knowledge.

🗓️ 22-23 June 2027

#singlecell #spatialbiology #spatialtranscriptomics
Norwich Single-Cell and Spatial Symposium 2027
Bringing together the international single-cell and spatial community for a two-day discussion across model and non-model systems.
okt.to
September 8, 2026 at 9:00 AM
scilifelab.se
Advanced #3Dimaging and #SpatialTranscriptomics are brought together to better understand #PulmonaryHypertension – a life-threatening condition for which current treatments can slow disease progression and relieve symptoms, but not target the underlying cause. ↓ 🧪

www.scilifelab.se/news/combini...
Combining 3D imaging and spatial biology to understand pulmonary hypertension
Pulmonary hypertension is a life-threatening condition for which current treatments can slow disease progression and relieve symptoms, but not target the underlying cause. A demonstrator project…
www.scilifelab.se
September 3, 2026 at 6:04 AM
itmat.bsky.social
#SpatialNT-Seq to spatially co-map newly synthesized and pre-existing #RNA in intact tissues www.nature.com/articles/s41... @hao_wu_7 #SpatialTranscriptomics #RNAturnover #SpatialBiology #TranslationalScience
Spatial mapping of RNA turnover kinetics in the mouse brain - Nature Neuroscience
The authors developed spatial NT-seq to map the landscape of RNA turnover and stability regulation in the mouse brain, identifying the dentate gyrus as a turnover hotspot and revealing region-specific...
www.nature.com
September 1, 2026 at 7:31 PM
jennyoung.bsky.social
National University of Singapore | NUS CDE | ACRLE | Bia-Echo

@10xgenomics.bsky.social | Optics11Life

#SpatialMechanomics #Mechanobiology #SpatialBiology #SpatialTranscriptomics #Nanoindentation #AFM #ExtracellularMatrix #ReproductiveAging #OvarianBiology #OvarianAging #Aging

7/7
September 1, 2026 at 5:28 AM
jennyoung.bsky.social
Excited to share our lab's new preprint led by
@huanting-ong.bsky.social on paired-surface spatial mechanomics!

We link nanoindentation maps with #SpatialTranscriptomics to connect local tissue mechanics with molecular state.

🔗https://www.biorxiv.org/content/10.64898/2026.08.29.748050v1

🧵1/7
Paired-Surface Spatial Mechanomics workflow
September 1, 2026 at 5:28 AM
alicefrolov.bsky.social
Rewiring of intercellular ligand-receptor communication in aged tissue

I am sharing a visualization exploring how intercellular signaling architecture is remodeled with chronological age.

#CellCommunication #LigandReceptor #SingleCellTranscriptomics #SpatialTranscriptomics #Stromalniche
Rewiring of intercellular ligand-receptor communication in aged tissue I am sharing a visualization exploring how intercellular signaling architecture is remodeled with chronological age. The figure ("Log2 fold-change (old vs young) in signaling pair activity across niches; simulated data") uses a diverging lollipop layout with a dual-panel mirror, presenting ligand-side and receptor-side activity shifts in vertically aligned registers. This mirror design allows direct visual comparison of whether a given signaling pair is being driven predominantly by altered ligand availability, receptor expression, or coordinated changes in both. I want to emphasize at the outset that the underlying data are simulated. The magnitudes and directionality, however, are parameterized to reflect trends repeatedly reported in the CellChat and CellPhoneDB-based literature on aged niches, so the figure is intended as an illustrative scaffold rather than an empirical claim. Several patterns are worth highlighting for discussion. Pro-inflammatory axes such as TNF-TNFRSF1A and CCL2-CCR2 display positive log2 fold-changes, consistent with the inflammatory remodeling and myeloid recruitment characteristic of aged stromal compartments. Conversely, WNT and NOTCH ligand-receptor pairs trend negative, mirroring reported attenuation of niche-derived regenerative and self-renewal cues. TGFB1-TGFBR2 shows a positive shift concordant with fibrotic reprogramming. The mirror arrangement makes clear that certain pairs are receptor-limited in the aged condition, which has implications for how one interprets deconvolved communication probabilities. Methodologically, I would welcome perspectives on normalization strategies for cross-niche comparison, particularly how to control for compositional shifts in cell-type abundance that can confound inferred communication strength.
August 31, 2026 at 5:03 PM
nonchev.bsky.social
#AIforScience #VirtualSpatialTranscriptomics #SpatialTranscriptomics #DigitalPathology #ComputationalPathology #SpatialOmics #CancerResearch #PrecisionMedicine
August 29, 2026 at 8:08 AM
facebase.bsky.social
Nerves don't just wire up muscle - they help build it. New in FaceBase: single-cell, bulk RNA-seq, and SeqFISH showing trigeminal nerve-derived GDF11 shaping soft palate muscle architecture. @ccmb.usc.edu #craniofacial #devbio #scRNAseq #spatialtranscriptomics

www.facebase.org/2026/08/25/r...
New release: Sensory nerve-derived signaling coordinates oropharyngeal structural organization that supports suckling and vocalization in neonatal mice
A new dataset from the Chai lab at the University of Southern California is now available in FaceBase, combining single-cell RNA sequencing, bulk RNA sequencing, and SeqFISH spatial transcriptomics to...
www.facebase.org
August 27, 2026 at 8:19 PM
nalcala.bsky.social
... this matches #spatialtranscriptomics patterns: supra-carcinoids actually tend to have restricted supra-carcinoid regions forming ecological niches with fibroblasts and macrophages, coexisting with regions from another group. Supra-carcinoids thus probably evolve from other groups
August 27, 2026 at 12:55 PM
ysanchez.bsky.social
We're excited to share our latest study on severe #preeclampsia using #singlecell and #spatialtranscriptomics to map cellular changes in space!

www.science.org/doi/10.1126/...
Spatially resolved fetal and maternal cell contributions to severe preeclampsia across gestation
Fetal and maternal contributions to severe preeclampsia unraveled in space and time with single-cell and spatial transcriptomics.
www.science.org
August 17, 2026 at 10:55 AM
sigtrans-sttt.bsky.social
Findings from a multicenter real-world study showed that T-TACE exerts superior clinical efficacy & safety vs D-TACE in BCLC stage B/C #HCC, while #SpatialTranscriptomics revealed potential mechanistic insights.
#STTT #OpenAccess: doi.org/10.1038/s413...
Temperature-sensitive liquid embolic agent transarterial chemoembolization versus drug-eluting bead transarterial chemoembolization for BCLC Stage B/C hepatocellular carcinoma: a multicenter real-world study and spatial transcriptomics profiling (CHANCE 2515)
August 15, 2026 at 3:00 AM
fiosgenomics.bsky.social
Does your study require #spatialtranscriptomics?
We have a sample report available demonstrating how #bioinformatics can help!
Request the report today at:
https://www.fiosgenomics.com/spatial-transcriptomic-analysis-report
August 14, 2026 at 7:30 AM
haoyin.bsky.social
A must-read for #SpatialTranscriptomics cell type deconvolution methods👹

5 large categories, 67 methods!🤠
Regression
Dimensionality reduction
Bayesian
Optimal transport
Deep learning

#NatureRevGenet 2025
www.nature.com/articles/s41...
August 12, 2026 at 10:53 AM
alforrest.bsky.social
Submit a poster for #HCA2026Asia!!

Poster abstracts remain open until 13 September, and submissions will be accepted until venue capacity is reached, so don't wait too long!

#SingleCell #SpatialTranscriptomics #HumanCellAtlas

events.humancellatlas.org/2026asia/abs...
August 9, 2026 at 11:06 PM
saurlab.bsky.social
🚀 Excited to share Cellpin for #SpatialTranscriptomics! Led by P. Putze & D. Lucarelli with @fabian_theis. Outperforms 6 methods for gene prediction, scales to atlas-size references, and boosts cell-state resolution in full-transcriptome Atera data. doi.org/10.64898/202...
August 9, 2026 at 1:34 PM
svanuytven.eurosky.social
Weekly reads 3/08/26:
How tumors talk to their surroundings, and how we’re learning to listen

behindthebioinformatics.substack.com/p/weekly-rea...

#SpatialTranscriptomics #SingleCell #CancerResearch #ComputationalBiology #FoundationModels
Weekly reads 3/08/26
How tumors talk to their surroundings, and how we’re learning to listen
behindthebioinformatics.substack.com
August 9, 2026 at 8:33 AM
carlus-2024.bsky.social
🧬 Foundational Spatial 'Omics Analysis – 9 modules in 3 days – September 28–30, 2026.
👉 Module 3 – "Understanding Your Platform Data Outputs."
+info: www.linkedin.com/feed/update/...
#SpatialOmics #SpatialTranscriptomics #Bioinformatics #SingleCell #Genomics #ComputationalBiology
July 31, 2026 at 3:17 PM
carlus-2024.bsky.social
🧬 « Fondements de l’analyse spatiale omic » - 9 modules en 3 jours - 28 au 30 septembre 2026.
👉 Module 3 - "Comprendre les données de sortie de votre plateforme."
+ infos ici: www.linkedin.com/feed/update/...
#SpatialOmics #SpatialTranscriptomics #Bioinformatics #DataManagement
July 31, 2026 at 2:59 PM
itmat.bsky.social
Plasticity in #CellCellCommunication may be central for how cell fate is robustly established in complex patterned tissues doi.org/10.1038/s415... @ksusztak.bsky.social #SingleCellRNASequencing #SpatialTranscriptomics #KidneyDevelopment
Single-cell spatial mapping of human kidney development implicates the microenvironment in guiding cell fate decisions - Nature Genetics
The spatial organization of human kidney development is explored using single-cell RNA sequencing and spatial transcriptomics, highlighting the crucial role of microenvironmental signals in guiding ce...
doi.org
July 31, 2026 at 11:35 AM