GESTALT

Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE - Nature Methods iSCALE leverages histology and spatial transcriptomics to infer gene expression at super resolution in large tissues.

iSCALE

www.nature.com/articles/s41...

Imaging-based multimodal profiling of single cells with STAMP Nature Reviews Genetics, Published online: 21 August 2025; doi:10.1038/s41576-025-00891-6In this Tools of the Trade article, Kellie Wise and Anna Pascual-Reguant introduce STAMP (single-cell transcriptomics analysis and multimodal profiling), which harnesses imaging to measure RNA and/or protein expression in fixed cells or nuclei.

New online! Imaging-based multimodal profiling of single cells with STAMP

Imaging-based multimodal profiling of single cells with STAMP - Nature Reviews Genetics In this Tools of the Trade article, Kellie Wise and Anna Pascual-Reguant introduce STAMP (single-cell transcriptomics analysis and multimodal profiling), which harnesses imaging to measure RNA and/or ...

Very proud of these two!

Anna Pascual Reguant | Kellie Wise

A beautiful collaboration with Jasmine Plummer & Holger Heyn

CNAG | St Jude Children’s Research Hospital

#STAMP

Imaging-based multimodal profiling of single cells with STAMP | Nature Reviews Genetics

www.nature.com/articles/s41...

Congrats @hoheyn.bsky.social , @lgmartelotto.bsky.social and team!

Tracing colorectal malignancy transformation from cell to tissue scale The transformation of normal intestinal epithelium into colorectal cancer (CRC) involves coordinated changes across molecular, cellular, and architectural scales; yet, how these layers integrate remai...

Tracing colorectal malignancy transformation from cell to tissue scale

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

STAMP brings us non-destructive single-cell profiling without the sequencing No sequencer needed: Imaging based single-cell multiomics

STAMP brings us non-destructive single-cell profiling without the sequencing

www.omic.ly/stamp-brings...

Counting my lucky stars⭐️that not only do I get to work with these amazing scientists Jiwoon Park @christophermason.bsky.social but also give fun @cshlnews.bsky.social lectures together💪.Big thank you to @lgmartelotto.bsky.social Nicholas Navin Julea Vlassakis for uniting this #singlecell #dreamteam

Integrating 12 Spatial and Single Cell Technologies to Characterise Tumour Neighbourhoods and Cellular Interactions in three Skin Cancer Types Cutaneous squamous cell carcinoma (cSCC), basal cell carcinoma (BCC), and melanoma, the three major types of skin cancer, account for over 70% of all cancer cases. Despite their prevalence, the skin c...

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

Don’t forget to register to the seminar on June 27 and July 25:

GESTALT - Seminar Series

June 27 - 2025: Dr. Fei Chen
July 25 - 2025: Dr. Hanchen Wang

Please visit the Seminar Series Webpage for more information and registration: globalspatial.org/seminar-seri...

STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging Single-cell transcriptomics analysis and multimodal profiling (STAMP) by imaging enables single-cell analysis of cells in suspension without the need for sequencing. The markedly reduced costs and fle...

Awesome work by awesome people! Endless innovation by @lgmartelotto.bsky.social and team.

Can’t wait to try it 💪

STAMP:Single cell Transcriptomics Analysis & Multimodal Profiling-cheap scprofiling-MILLIONS of cells, multimodal, pertubation expts & tissue atlas'ing at scale.Thx to brilliant colleagues @lgmartelotto.bsky.social Holger Heyn & our amazing teams. @cellpress.bsky.social www.cell.com/cell/abstrac...

“STAMP allows us to profile a million cells simultaneously, compared to tens of thousands typical of current methods, making it far more scalable,” said @jasmineplummer.bsky.social, PhD, St. Jude Center for Spatial Omics director.

STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging @cellcellpress.bsky.social @lgmartelotto.bsky.social @hoheyn.bsky.social
www.cell.com/cell/fulltex...

👩‍🔬The lead authors of the study are Dr. @pascual-reguant.bsky.social & Emanuele Pitino (CNAG) with Felipe Segato Dezem (@stjuderesearch.bsky.social)

Corresponding authors: Dr. @hoheyn.bsky.social (CNAG), Dr. @jasmineplummer.bsky.social (St. Jude) & Dr. @lgmartelotto.bsky.social (Univ. of Adelaide)

Team Seeks Adoption of Sequencing-Free, Imaging-Based Single-Cell Profiling Method Developed by researchers in the US, Spain, and Australia, STAMP promises to reduce single-cell experiment costs almost 50-fold by eliminating the need for sequencing.

www.genomeweb.com/sequencing/t...

Cell simulation as cell segmentation - Nature Methods Proseg is a segmentation approach for single-cell spatially resolved transcriptomics data that uses unsupervised probabilistic modeling of the spatial distribution of transcripts to accurately segment...

www.nature.com/articles/s41...

ezSingleCell: an integrated one-stop single-cell and spatial omics analysis platform for bench scientists - Nature Communications ezSingleCell is an interactive and user-friendly application for the analysis of single-cell and spatial omics data, without the need for programming expertise. Here, authors integrated top-performing...

www.nature.com/articles/s41...

tidyplots is an R package to generate publication-ready plots for scientific papers tidyplots.org/ #rstats

Excited to share a new algorithm that we have been working on over the last year.

💡 idea is to extend mutual nearest neighbors for
#spatial data. We call it spatial mutual nearest neighbors (spatialMNN) 😄

Thank you @haowen-zhou.bsky.social @pratibha-panwar.bsky.social who led this work! 👏 🧬🖥️🧪

It is so nice to spend quality time with your favorite people in the world before the end of the year!

@jasmineplummer.bsky.social @alexswarbrick.bsky.social

At Multi-Ome 2024

Btw: my best pic yet!

Damsel: analysis and visualisation of DamID sequencing in R AbstractSummary. DamID sequencing is a technique to map the genome-wide interaction of a protein with DNA. Damsel is the first Bioconductor package to prov

Happy to see our Damsel @bioconductor.bsky.social package published in Bioinformatics. Great work putting together this DamID sequencing and package from student Caitlin Page. Thanks to collaborators too @lonsbio.bsky.social

academic.oup.com/bioinformati...

It is important to clarify what you mean by real science. If ‘real’ refers to methodologically sound, evidence-driven, and reproducible research, then funding may not directly define the quality of the science, but it certainly influences the scale, tools, and opportunities available for doing it.

easySCF: A Tool for Enhancing Interoperability Between R and Python for Efficient Single-Cell Data Analysis AbstractSummary. This study introduces easySCF, a tool designed to enhance the interoperability of single-cell data between the two major bioinformatics pl

#singlecell to #spatial converts .. means a lot more python than r… great tool to help transition academic.oup.com/bioinformati...

MCGAE: unraveling tumor invasion through integrated multimodal spatial transcriptomics Abstract. Spatially Resolved Transcriptomics (SRT) serves as a cornerstone in biomedical research, revealing the heterogeneity of tissue microenvironments.

MCGAE: unraveling tumor invasion through integrated multimodal spatial transcriptomics #SingleCell 🧬🖥️ academic.oup.com/bib/article/...

Whole-brain spatial transcriptomics 🧪🤯
Congratulations to all the team @peruhlen.bsky.social

Cellular atlases are unlocking the mysteries of the human body Scientists reflect on insights from the Human Cell Atlas.

The Human Cell Atlas is yielding detailed maps of human tissues and systems throughout life, along with methods to handle single-cell data. Four scientists reflect in Nature on how the project is transforming our understanding of human biology. 🧪

Sainsc: A Computational Tool for Segmentation‐Free Analysis of In Situ Capture Data Spatially resolved transcriptomics methods can now profile the entire transcriptome, at full organism scale with nanometre resolution. Analysis frameworks that can efficiently and intuitively process....

Cool tool for segmentation free #spatial #transcriptomics onlinelibrary.wiley.com/doi/10.1002/...

Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus Spatially mapping the transcriptome and proteome in the same tissue section can significantly advance our understanding of heterogeneous cellular processes and connect cell type to function. Here, we ...

The second preprint presents an experiment workflow and a broadly applicable computional framework to integrate sequencing-based and imaging-based spatial omics data for the SAME tissue slide to construct a single cell spatial omics atlas.

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

GitHub - theislab/spapros: Python package for Probe set selection for targeted spatial transcriptomics. Python package for Probe set selection for targeted spatial transcriptomics. - theislab/spapros

#LocationLocationLocation! Theis &co share @ Nature Methods @natureportfolio.bsky.social a probe set selection pipeline to identify cell types using spatial single cell omics! And it comes with its Python package (github.com/theislab/spa...) 😌💪 👉 doi.org/10.1038/s41592-024-02496-z