#SpatialTranscriptomics

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 👩‍🔬

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

#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

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?

Spatial mechano-transcriptomics👹 Overlay image-based cell mechanics inference [Segmentation with Multi-junctional molecular avg▶️ Circular arc polygon tiling for cell contacts▶️ Cellular pressure, junctional tension, stress tensor] with imaging-based #SpatialTranscriptomics (SeqFISH 387-gene) Spatially-resolved ligand-receptor pair analysis ➡️ molecular determinants of interfacial tension in 🐭Embryonic🧠#BoundaryFormation🤠 Can we run in silico knockout in this framework?😁 @Hallou_Lab @he_ruiyang @bidumit @naturemethods 2025

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

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

Excited to share the first work during my PhD on spatiotemporal gene expression of human embryonic development and hematopoiesis in an organoid platform. We used #scRNAseq and 10x Visium #SpatialTranscriptomics to define the development process. 1/

Imaging-based #SpatialTranscriptomics #Segmentation Segger 👉Attention-based #GraphNeuralNetwork 👉Learn a transcript-cell/boundary joint latent space 👉Unassigned transcripts➡️fragments➡️ median 20 transcripts/fragment vs 50 transcripts/cell vs Baysor BIDCell CellPose 10X Cell/Nuclei protocol 30 times faster than Baysor (on 4x @NVIDIAAI A100 GPU...🤧💸💸💸🤑) @HeidariElyas @MoritzGerstung bioRxiv 2025

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

#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

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

🚨New #SpatialTranscriptomics #Bioinformatics data resource out in @naturemethods. SODB, a platform with >2,400 manually curated spatial experiments from >25 spatial omics technologies & interactive analytical modules. This🧵will walk you through all the features of SODB [1/33]

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

STCellbin Use Nuclei+Cell Membrane/Wall stains to improve #CellSegmentation & single-cell-resolved #SpatialTranscriptomics Tailored for #StereoSeq, but likely implementable for other ST methods Susanne Brix & Xun Xu labs @GigaByteJournal 2024

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

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

Light-Seq an inexpensive technology that enables to visually identify interesting subsets of cells, sequence their transcriptomes, and further image the same cells after sequencing. #SingleCell #RNAseq #SpatialTranscriptomics

Check out our @PNASNews paper on 10K gene #spatialtranscriptomics by #MERFISH with ∼80% detection efficiency: We infer #RNAvelocity in situ + pseudotime to reveal genes with #cellcycle dependent expression + more #singlecell #bioinformatics #BigData

Excited to share our new preprint on #thalamus development! 🧠 We reveal how sensory and non-sensory circuits are specified early in embryogenesis using #mutiomics, #spatialtranscriptomics, #lineagetracing. @GLB_Lab @JPLopezAtalaya @NeuroAlc