#CosMx
LightNews LightNews
haoyin.bsky.social
Comparing Imaging-based #SpatialTranscriptimics methods

CosMx vs MERFISH vs Xenium
1k vs 500 vs 339 plex

FFPE👤Lung/Mesothelium Tumor Microarray

CosMX▶️highest transcript counts/cell
Xenium▶️lowest FDR & highest cell segmentation precision

bioRxiv 2024
www.biorxiv.org/content/10.1...
December 19, 2024 at 12:21 PM
caffeinegobbo.bsky.social
In all their shiny glory, here's my #masks #oc, Cosmx!
November 16, 2025 at 9:33 AM
haoyin.bsky.social
In imaging-based spatial transcriptomics (Xenium CosMx), 40% RNAs are Not assigned to segmented cells

This amazing preprint @fabiantheis.bsky.social studies the origin, heterogeneity & biological inference (Modeling cell protrusion/contacts😎) of unassigned RNAs

www.biorxiv.org/content/10.6...
March 6, 2026 at 12:11 PM
haoyin.bsky.social
Comparative analysis of commercial Imaging-based #SpatialTranscriptomics methods

Xenium
CosMx 1k
MERSCOPE

Tissue Microarray
17 tumor+16 normal tissue

Transcript count
vs Reference RNAseq
Segmentation accuracy
Cell type annotation

#NatComms 2025
www.nature.com/articles/s41...
December 1, 2025 at 12:52 PM
fabiantheis.bsky.social
Need to design your next Xenium/CosMx/Merfish experiment? Spapros, now out @naturemethods, allows for probe set selection for target spatial tx. Led by @KuemmerleLouis, it optimizes both cell type ID & within-cell type variation. nature.com/articles/s41592-024-02496-z github.com/theislab/spapros
November 20, 2024 at 7:50 AM
haoyin.bsky.social
Comparing single-cell #SpatialTranscriptomics methods on FFPE human tumor #TissueMicroArray

CosMx 1k vs MERFISH 500 vs Xenium-UM/-MM 339
93 common genes

lung adenocarcinoma
pleural mesothelioma

Corr. Bulk RNAseq, GeoMx

#NatureComms 2025
www.nature.com/articles/s41...
September 28, 2025 at 12:22 PM
haoyin.bsky.social
#SpatialTranscriptomics #Atherosclerosis

A first CosMx 1k plex single-cell map of👤coronary atherosclerosis😆

From Adaptive intimal thickening to Large Atheromatous plaque with intralesional fibrosis

bioRxiv 2025
www.biorxiv.org/content/10.1...
April 6, 2025 at 11:16 AM
albertvilella.bsky.social
Bruker's Spatial Multiomics update open.substack.com/pub/albertvi...
Bruker's Spatial Multiomics update
Bruker CosMx and how it compares to 10X Genomics Xenium
open.substack.com
May 19, 2025 at 8:01 AM
haoyin.bsky.social
1st single-cell #SpatialTranscriptomics map of human coronary #Atherosclerosis published in peer-reviewed format🤠

CosMx 1k + GeoMx @brukerspatial

Immune cell-focused analysis

Use CosMx data to deconvolve GeoMx cell composition...😆

#EmboMolMed 2025
www.embopress.org/doi/full/10....
November 11, 2025 at 12:15 PM
alforrest.bsky.social
Wow head-to-head comparison Visium HD FFPE, CosMx 6K, Xenium 5K, Stereo-seq v1.3 and Visium HD FF profiling on HGSOC and HCC. Heads-up @GESTALT_sp hopefully can save community some $$$$
December 30, 2024 at 9:36 AM
haoyin.bsky.social
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

#NatComm 2025
www.nature.com/articles/s41...
October 24, 2025 at 10:45 AM
ankuroncofetal.bsky.social
Excited to share our updated Renoir @biorxivpreprint.bsky.social with Hamim from IITK to predict spatial cell-cell interactions
New additions:
- Benchmarking data
- Applicability on SMI (CosMx) data
- Identification of stem-like MUC6 cancer cells in oncofetal niche
www.biorxiv.org/content/10.1...
November 16, 2024 at 10:50 AM
jsantoyo.bsky.social
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...
Source: https://www.biorxiv.org/content/10.1101/2024.11.25.625243v1
December 1, 2024 at 8:05 PM
haoyin.bsky.social
#SpatialOmics

The Spatial Atlas of Human Anatomy (SAHA): A Multimodal Subcellular-Resolution Reference Across Human Organs

15 M cells
100 donors
10 organs

Liver
Pancr
Bone marr
Lymph node
PBMC
Prost
Stoma
ILeum
Colon
Appendix

CosMX 1k 6k WTA
Xenium

bioRxiv 2025
www.biorxiv.org/content/10.1...
June 24, 2025 at 7:03 PM
haoyin.bsky.social
CODA
CrOss-sample alignment & spatially Differential gene Analysis for #SpatialTranscriptomics

Global rigid alignment➡️
Shared coordinate➡️
RGB image rep➡️
LightGlue common domain➡️
Local nonlinear alignment

Visium MERFISH Stereoseq STARmap RIBOmap CosMx

bioRxiv 2025
www.biorxiv.org/content/10.1...
June 19, 2025 at 11:58 AM
haoyin.bsky.social
#Polyploidy
#HNSCC

TREM2-Expressing Multinucleated Giant Macrophages Are a Biomarker of Good Prognosis in Head and Neck Squamous Cell Carcinoma

Cool CosMx single-cell spatial (64-plex) immunophenotyping🤠

#CancerDiscov 2024
aacrjournals.org/cancerdiscov...
September 24, 2026 at 12:08 PM
haoyin.bsky.social
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...
February 5, 2024 at 12:49 PM
carmonation.bsky.social
Visualising the impact of wounding on cancer cells and the tumor microenvironment at single-cell resolution in situ!

Happy to share updated paper with new spatial transcriptomics of human skin tumors using CosMx 6'000-gene panel. All data and code are available.

www.biorxiv.org/content/10.1...
https://www.biorxiv.org/content/10.1101/2024.05.31.596823v2.full
February 24, 2025 at 3:34 PM
cnag-eu.bsky.social
🗓️Save the date: March 25, 5 PM – new webinar by @brukerspatial.bsky.social

🗣️Speaker: Our PhD student, Emanuele Pitino
➡️'STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging, with Dr. @pascual-reguant.bsky.social from #CNAG

go.brukerspatialbiology.com/CosMx-STAMP-...
March 19, 2025 at 12:50 PM
arcturusjackal.bsky.social
I hate the CosMx protocol. But it does generate prettier inital scan images...
September 19, 2025 at 12:00 AM
lcolladotor.bsky.social
Evelyn Metzger from Bruker is now presenting about www.biorxiv.org/content/10.1... and the #AtoMx™️ cloud solution for analyzing #CosMx data

#SpatialBiology
December 5, 2024 at 7:19 PM
tmpentimalli.bsky.social
www.cell.com/cell-systems...

CosMx data by @brukerspatial.bsky.social
Second harmonics by Andrew Woehler
Immunofluorescence by @sonjafritzsche.bsky.social and @josenimo.bsky.social in Fabian Coscia lab
STIM for 3D alignment by @preibischs.bsky.social @nukappa.bsky.social et al (coming very soon!)
Combining spatial transcriptomics and ECM imaging in 3D for mapping cellular interactions in the tumor microenvironment
Pentimalli et al. extend imaging-based spatial transcriptomics to 3D and combine it with ECM profiling. The multimodal analysis of cellular neighborhoods in a clinical lung adenocarcinoma sample revea...
www.cell.com
April 16, 2025 at 10:40 AM
ausbiocommons.bsky.social
Learn how to analyse #SpatialOmics data in #R in this hands-on workshop.

Join Sarah and Fred as they guide you through the process of visualising gene expression from CosMx, Xenium experiments within tissue samples.

🗓️ 28 - 29 Oct 2025
👉 More info: www.biocommons.org.au/events/spati...
WORKSHOP: Spatial omics — Australian BioCommons
Learn how to analyse data from in situ spatial (e.g. CosMx, Xenium) experiments with Seurat in R to visualise gene expression within tissue samples. More information Apply here
www.biocommons.org.au
August 19, 2025 at 11:16 PM
haoyin.bsky.social
SpatialData
spatialdata.scverse.org/en/latest/

Establish a global common coordinate framework->
Multi-modal #SpatialOmics integration
Align multislice for 3D #SpatialOmics

Work with
(RNA) Visium Xenium CosMx MEFISH
(protein) CycIF MIBI-TOF IMC

#Naturemethods 2024
www.nature.com/articles/s41...
March 22, 2024 at 11:37 AM
hoxinsocks.bsky.social
"Yes."

nanostring-biostats.github.io/CosMx-Analys...
July 10, 2026 at 7:07 AM