#spatialTranscriptomics

Comparative analysis of commercial Imaging-based #SpatialTranscriptomics methods Xenium CosMx 1k MERSCOPE Tissue Microarray 17 tumors + 16 normal tissues Transcript count Corr. with reference bulk TCGA GTEx RNAseq or scRNAseq Segmentation (Precision Recall F1 score) Accuracy: Elongated < Sparse < Dense cells Cell type annotation 2024 CosMx @brukerspatial protocol (vs 2023)▶️ 10-fold ⬆️sensitivity!😮 MERSOPE sensitive to RNA quality @GoodsBrittany @NatureComms 2025

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

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

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 &amp; single-cell-resolved #SpatialTranscriptomics Tailored for #StereoSeq, but likely implementable for other ST methods Susanne Brix &amp; Xun Xu labs @GigaByteJournal 2024

Systematic comparison of 11 sequencing-based #SpatialTranscriptomics methods A must-read for spatial omics researchers🤠 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?😁 A standard benchmarking pipeline ▶️Molecule-capture efficiency (per unit area) ▶️Molecule lateral diffusion ▶️Clustering/Cell annotation (Seurat still outperforms or PRECAST😯) ▶️Marker gene detection ▶️Cell-to-cell communication (no consistent results found) 💰Fig 4f Affordability Xiaodong Liu & Luyi Tian labs @naturemethods 2024 @ethanxdliu @Luyi_T + cadasSTre, a website for raw/processed data #OpenScience

#CellCharter A powerful single-cell #SpatialTranscriptomics analysis framework Graph-based #DeepLearning Spatial cluster: Cell type Different expression Neighborhood enrichment AND Shape!!!👹 - curl/elongation/linearity/purity #VariationalAutoEncoder for dimension reduction, batch correction & multi-technical platform (CosMx/MERFISH/#ImagingMassSpectrometry)/Multiomic integration Spatially-resolved #LungCancer Hypoxia & Tumore-associated neutrophil signatures->Prognostic values for NSCLC Computationally efficiency->Scalability @MarcoVarrone @loganawalsh @CirielloLab @NatureGenet 2024

Benchmarking 6 Imaging-based #SpatialTranscriptomics methods #MolecularCartography #Xenium #MERSCOPE #MERFISH #EELFISH #STARmapPLUS 🐭🧠 Mutually exclusive co-expression rate/MECR Who wins👑? #CosMx Not even in short list😔 @satijalab bioRxiv 2024

De-spot Projecting sc-/sn-RNAseq (paired/unpaired) to #SpatialTranscriptomics Visium ST Stereo-seq MERFISH-> Spatial Multi-modality Data Sharpen the spatial cell-type boundaries Improve detection of low-proportion cell-type spatial domains Jian Liu lab @CellRepMethods 2024

Mapping the transcriptome: Realizing the full potential of spatial data analysis A must-read for #SpatialTranscriptomics beginners Learn from Geographical science #SpatialAutocorrelation #GeographicallyWeightedRegression @LZormpas @sjcockell Cell 2023

Video tutorial -- DBiT-seq protocol for spatial transcriptome and multi-omics sequencing (Fan Lab @ Yale) #spatialomics #spatialbiology #spatialtranscriptomics

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

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

C-SIDE Cell type-specific inference of differential expression in #SpatialTranscriptomics 👉Work for both Sequencing- & Imaging-based ST 👉Need single-cell reference for cell typing 👉Histological features as covariates 👉Pixel-based, Segmentation-free differentially expression analysis "12.6% double cell type pixels out of 3,790 total pixels" in a MERFISH brain🤓 @rafalab @insitubiology @naturemethods 2022

I am updating my lecture slides on #spatialtranscriptomics to use author names + remove journal names to de-emphasize brands and re-emphasize people per #HHMI recs. In the process, I realized ALL the seminal techdev work has been led by co-first authors contributing equally 🧵1/3

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 use our lab's recently published #spatialtranscriptomics #dataanalysis tool MERINGUE to complement #singlecell clustering analysis to look for spatial #geneexpression patterns within cell-types in the mouse cortex: #bioinformatics #Rstats #codetutorial

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 👩‍🔬

Excited to share our latest study in Cardiovascular Research (@escardio)! 🎉 Using CosMx WTX #spatialtranscriptomics (@brukerspatial) and paired plaque-PBMC #scRNAseq, we reveal critical cellular drivers of plaque instability beyond stenosis severity.

Recent advances in differential expression analysis for single-cell RNA-seq and spatially resolved transcriptomic studies. #SingleCell #scRNAseq #SpatialTranscriptomics #DifferentialExpression #ToolsReview #BriefingsInFunctionalGenomics