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! biorxiv.org/cgi/content/shor…
See below the #tweetorial from our very own @handlerkristina 👩🔬
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.
🔗biorxiv.org/content/10.64898…
🧵1/7
Curious about what we can do? #SpatialTranscriptomics - all mRNAs spatially resolved. See our showcase: buff.ly/2sXrziN
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
nature.com/articles/s41588-0…
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
nature.com/articles/s41467-0…
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 DR.SC 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
nature.com/articles/s41592-0…
+ cadasSTre, a website for raw/processed data #OpenScience
genographix.com/home
DeepSpaceDB
genomics.virus.kyoto-u.ac.jp…
>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
academic.oup.com/nar/article…
In this blog post, I compare deconvolution analysis using STdeconvolve to clustering analysis on multi-cellular pixel-resolution #spatialtranscriptomics data: jef.works/blog/2022/05/03/de…
What do you think? Try it out for yourself!
#RStats #Bioinformatics #dataanalysis #dataviz
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
elihei2.github.io/segger_dev…
vs Baysor BIDCell CellPose 10X Cell/Nuclei protocol
30 times faster than Baysor (on 4x @NVIDIAAI A100 GPU...🤧💸💸💸🤑)
@HeidariElyas @MoritzGerstung bioRxiv 2025
biorxiv.org/content/10.1101/…
Many #SpatialTranscriptomics tools are out there! Which performs best? Which runs fastest?
A nice resource here😆👇
16 clustering methods
SpatialPCA
DR.SC
SpaGCN
BANKSY
GraphST
STAGATE
SEDR
PRECAST
conST
DeepST
CCST
BASS
ADEPT
SpaceFlow
BayesSpace
ConGI
10 datasets Visium ST Slide-seqV2 Stereo-seq STARmap MERFISH (No CosMx🥺)
Spatial continuity analysis😃
1⃣Average silhouette width
2⃣Spatial chaos score
3⃣Percentage of abnormal spots
Performance (+SPACEL PASTE PASTE2 SPIRAL STAligner GPSA) over
1⃣Batch correction
2⃣Multi-slice integration
3⃣3D reconstruction
Xin Maizie Zhou lab @GenomeBiology 2024
genomebiology.biomedcentral.…
I used gganimate in #Rstats to tell a story about #singlecell #spatialtranscriptomics #bioinformatics #dataanalysis
Code: jef.works/blog/2021/08/12/st…
If a picture is worth a 1000 words, perhaps an animation is worth a million? What's your interpretation of this #dataviz story?
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
TransformerST
#SpatialTranscriptomics
Vision transformer
Adaptive graph transformer
Cross-scale internal graph network
Image-gene co-representation:
Gene expression+Spatial coordinates+Histologic images
"could achieve super-resolved resolution of a single cell per subspot" w/o scRNAseq reference
Note for Lung Microvascular researchers with #VISIUM
✅stLearn SpaGCN TransformerST
@BriefingBioinfo 2024
academic.oup.com/bib/article…
If you are a #SpatialOmics learner like me, this is a particularly useful, timely piece of reading 😀
🚨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]
We're excited to release a #scanpy update for the analysis and visualization of #spatialTranscriptomics data, focussing on @10xGenomics Visium and MERFISH, thx @g_palla1. Tutorial at nbviewer.jupyter.org/github/…
Support for different data types and integration with #scRNAseq soon!
scType
Marker-based cell type annotation for #SpatialTranscriptomics Visium Slide-seq
Use positive + negative markers (from scTypeDB database with previously scRNAseq-identified cell type markers or custom marker genes), instead of deconvolution.
R & Python
github.com/kris-nader/sp-typ… or github.com/kris-nader/sc-typ…
Mitro Miihkinen lab Bioinformatics 2024 @mitroe
academic.oup.com/bioinformat…
#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
nature.com/articles/s41592-0…
Thrilled to share our #bioinformatics tool for aligning #spatialtranscriptomics data using #LDDMM across technologies, partial matched tissues, to 3D atlas
📰 biorxiv.org/content/10.1101/…
🖥️ github.com/JEFworks-Lab/STal… #Python
Congrats @kalen_clifton @manjari_017 w/ collab @UCLA @JHUBME
In our latest study, we look at how storing kidneys on ice before transplant can cause damage over time. We use #spatialtranscriptomics to characterize cold ischemia injury at multiple time points to reveal compartment-specific changes
Preprint: biorxiv.org/content/10.1101/…
🧵👇 1/n
Thrilled to share our #Bioinformatics work led by @bf_miller_ +team. We deconvolve multicellular pixel resolution #spatialtranscriptomics data w/o #singlecell references to recover cell-type specific spatial patterns.
📰 biorxiv.org/content/10.1101/…
🖥️ github.com/JEFworks-Lab/STde… #RStats
