#SpatialTranscriptomics

In this blog post, I use simulations to demonstrate the difference between clustering vs deconvolution #bioinformatics analysis using STdeconvolve when applied to multi-cellular pixel-resolution #spatialtranscriptomics data: #RStats #dataanalysis #dataviz

We are excited to share our new preprint about our development of a new #spatialTranscriptomics method (sphere-sequencing) to unveil local tissue microenvironments at single cell resolution! See below the #tweetorial from our very own @handlerkristina 👩‍🔬

New preprint from our group: Benchmarking Computational Integration Methods for Spatial Transcriptomics Data. @jenny589446011 @GarmireGroup Preprint here: #SingleCell #SpatialTranscriptomics #clustering #Bioinformatics

Stoked to share our new paper w/ @TiroshLab in @NatureGenet! Using spatial multi-omics we characterized two distinct modes of p-EMT in HNSCC, each with their own distinct ecosystems and drivers. #SpatialTranscriptomics #HNSCC #Visium #CODEX #EMT

#SpatialRNAEncyclopedia Patho-DBiT #SpatialTranscriptomics FFPE Spatial Co-mapping of RNA Expression Splicing editing SNV AND ncRNAs (miRNA lncRNA rRNA snRNA snoRNA & more)👹 in situ polyA tailing all RNAs 10 μm/px (near single cell)➡️ >2000 genes > 6000 UMIs/px Lymphoma @Zhiliang_Bai @DrMingyaoLi @YiXing77 @JunLuLab @MinaXu7 @RongFan8 @CellCellPress 2025

DeepSpaceDB >2k #SpatialTranscriptomics Visium samples 👉Interactive, downloadable data analysis QC➡️ manual/LLM image annotation➡️ in-sample or cross-sample spot clustering BASS BayesSpace➡️ Spatially variable genes singleCellHaystack SPARK-X binSpect➡️ Cell type deconvolution RCTD SPOTlight 👉Cross-sample/Cross-study comparison 👉Analyze your own data 👉Database-wide gene/pathway inquiry @alexisvdb #NucAcidRes 2026

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 Gene detection sensitivity (CosMx performance...🙁) (Spatial) false positives Transcript-protein correlation Cell segmentation Cell type annotation & spatial alignment to CODEX Spatial clustering Spatial pathway enrichment @NatureComms 2025

I run through #coding a #spatialtranscriptomics analysis in #rstats to characterize how cell-types are organized in breast cancer using our #bioinformatics deconvolution tool STdeconvolve Check out the video + code along: #AcademicTwitter #CodingTutorial

Excited to share our lab's new preprint led by Ting @huanting_ong introducing paired-surface spatial mechanomics! We link nanoindentation stiffness maps with #SpatialTranscriptomics to connect local tissue mechanics with molecular state. 🔗 🧵1/7

#SpatialTranscriptomics #ThoracicAorticDisease Human aorta is a mm-thick layered organ (50~60 circumferential Elastic-contractile units in adult) Its lumen & adventitia sides receive different chemical/mechanical inputs Any phenotypic/signaling gradients of #SmoothMuscleCells across the aortic medial depth?😆👇 Here is a very cool & informative study from one of my most favorite scientists, Dr. Hiromi Yanagisawa @HYanagisawaLab 👏 Micro-biopsies RNAseq from 4 distinct layers in human aortic media 5 #BicuspidAorticValue + 4 Sporadic Extracellular Matrix signaling (FN1/VCAN/MGP/POSTN) enriched in innermost layer (Beautiful POSTN IHC😍) TGFβ BAV > Sporadic Inflamm Sporadic > BAV Mechanosensing in innermost layer Sporadic > BAV🥸 #AortaEd #JVSVS 2026 @JVascSurg

I used gganimate in #Rstats to tell a story about #singlecell #spatialtranscriptomics #bioinformatics #dataanalysis Code: If a picture is worth a 1000 words, perhaps an animation is worth a million? What's your interpretation of this #dataviz story?

Now online in @CD_AACR: #SpatialTranscriptomics of Intraductal Papillary Mucinous Neoplasms (#IPMN) of the Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential @Marta_Sans_ @Aiims1742 @MDAndersonNews

Spatial transcriptomics reveals ovarian cancer subclones with distinct tumour microenvironments Here we used #Visium #SpatialTranscriptomics to study the cellular makeup of #ovariancancer / #HGSOC. @anzgog @cancercouncilWA @ozsinglecells @10xgenomics

GOD IS GOOD! Today, I passed my #PhD Dissertation Defense!!! 🎉 Thank you to everyone who believed in me. Thank you to all my mentors, friends, and family. 🥰 I would not be where I am today without all of you. 🙏❤️ @SBS_UNTHSC #SpatialTranscriptomics #DoubleDocs @A_P_S_A

THRILLED to share our latest work at the @hoheyn lab: "SPOTlight: Seeded NMF regression to Deconvolute Spatial Transcriptomics Spots with Single-Cell Transcriptomes". THREAD (1/n) #singlecellcnag #spatialtranscriptomics #visium

Mapping isoforms and regulatory mechanisms from spatial transcriptomics data with SPLISOSM. #SpatialTranscriptomics #Isoforms @NatureBiotech

Curious about what we can do? #SpatialTranscriptomics - all mRNAs spatially resolved. See our showcase:

We really recommend you to read this article called: "Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity": #SpatialTranscriptomics

Want to visualize & create a website for your omics data (+CITEseq scATACseq #SpatialTranscriptomics)? Try ShinyCell2!😆 Compatible with data formats Seurat Signac ArchR Scanpy (other formats converted by sceasy) (also imaging-based ST data?😁) vs cellxgene WebAtlas Vitessce @OwenRackham @imouyang bioRxiv 2024

#SpatialTranscriptomics Optimizing Xenium @10xGenomics In Situ data utility by quality assessment & best-practice analysis workflows If you are a Xenium user, this is a must-read🔥 👉Segmentation: Cellpose + Baysor (Segmentation-free alternative: SSAM, Points2Regions) 👉Preprocessing: Library size normalization, log-transformation, scaling, k-nearest neighbors graph (all PCs + 16 neighbors), Louvain clustering 👉Spatially variable feature selection: Squidpy Moran's I, Seurat Moran's I, Sinfonia, SomDE, Giotto, Hotspot 👉Imputation: SpaGE, Seurat, Tangram, SpaOTsc 👉Spatial domain identification: binning-based strategy, Bansky, SPACEL Performance vs CosMX, Molecular cartography, MERFISH, MERSCOPE, high-sensitivity ISS @naturemethods 2025