GitHub - HiDiHlabs/ovrl.py: A python tool to investigate cell overlaps in imaging-based spatial transcriptomics data. A python tool to investigate cell overlaps in imaging-based spatial transcriptomics data. - HiDiHlabs/ovrl.py

We also released the ovrl.py tool to identify areas of cell overlaps in imaging-based spatial transcriptomic data (e.g. #Xenium, #MERSCOPE, #cosMX).
GitHub: github.com/HiDiHlabs/ov...

Systematic Benchmarking of High-Throughput Subcellular Spatial Transcriptomics Platforms Recent advancements in spatial transcriptomics technologies have significantly enhanced resolution and throughput, underscoring an urgent need for systematic benchmarking. To address this, we collecte...

The heroes we need and don't deserve - a great benchmarking resource comparing BGI's #stereoseq with @brukercorporation.bsky.social 's #CosMX 6k and @10xgenomics.bsky.social #VisiumHD and #Xenium 5k - Packed with lots of interesting metrics and observations, including transcript diffusion...

Sub-cellular Imaging of the Entire Protein-Coding Human Transcriptome (18933-plex) on FFPE Tissue Using Spatial Molecular Imaging Single-cell RNA-seq revolutionized single-cell biology, by providing a complete whole transcriptome view of individual cells. Regrettably, this was accomplished only for individual, tissue-dissociated...

Pretty impressive whole transcriptomics CosMx
#spatialtranscriptomics #cosmx

nanostring.com/products/cos...

www.biorxiv.org/content/10.1...

Point your analysts to nanostring-biostats.github.io/CosMx-Analys... to learn how to analyze #CosMx data 📊

#SpatialBiology

Evelyn Metzger from Bruker is now presenting about www.biorxiv.org/content/10.1... and the #AtoMx™️ cloud solution for analyzing #CosMx data

#SpatialBiology

Source: https://www.biorxiv.org/content/10.1101/2024.11.25.625243v1

NoButter: An R package for reducing transcript dis-persion in CosMx Spatial Molecular Imaging Data. #SpatialTranscriptomics #CosMx #TranscriptDispersion #R @biorxivpreprint.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...

Benchmarking Imaging-based #SpatialTranscriptomics on FFPE #TissueMicroArray

7 tumors + 16 normal tissues

#CosMx 1 panel
#Xenium 3 panels
#MERSCOPE 2 panels
>94 genes overlap

"CosMx transcript counts may be slightly inflated by false discoveries"🤕

bioRxiv 2023
www.biorxiv.org/content/10.1...

Intratumoral heterogeneity & Immune-tumor cell Zonation in #Glioblastoma

Integrative #SpatialTranscriptomics
#GeoMx #CosMx #Xenium +public #Visium

IDH1-WT tumors have more mesenchymal+progenitor-like cells than IDH1-mutant

Neuro-Oncology Advances 2023
academic.oup.com/noa/article/...

Human Stomach Cell Atlas

scRNAseq
#SpatialTranscriptomics #CosMx #Giotto

Great synthesis with past literature🤠

Gastric #Pericyte😆
1⃣#Pericrine Thrombospondin FGF
2⃣Spatial neighbor: KLF+ Fibroblasts > Endothelial Cell!?😯

#CellReports 2023
www.cell.com/cell-reports...

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😔

#bioRxiv 2024
www.biorxiv.org/content/10.1...

#Xenium vs #CosMX
Not a lawsuit, but a scientific duel

Best learning materials for #SpatialOMics users 2023 👏👏👏
Don't miss the Methods

Oh, the segmentation of vasculature🥺
I guess I need a seg. antibody for CosMX

bioRxiv 2023
www.biorxiv.org/content/10.1...

#Voltron
#SpatialOmics analysis suite
#R

Versatile with multi-resolution methods
#GeoMx #CosMx #Visium #Xenium #SpatialProteomics #ImagingMassSpectrometry

Spatial data-image registration with OpenCV
RCTD/MuSiC for cell-type deconvolution

#bioRxiv 2023
www.biorxiv.org/content/10.1...