GESTALT
@gestaltsp.bsky.social
Global Alliance for Spatial Technologies: an organized whole that is perceived as more than the sum of its parts. Democratizing Spatial-Omics Techs
iSCALE www.nature.com/articles/s41...
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.
nature.com
New online! Imaging-based multimodal profiling of single cells with STAMP
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.
nature.com
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...
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 ...
nature.com
Tracing colorectal malignancy transformation from cell to tissue scale www.biorxiv.org/content/10.1...
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...
biorxiv.org
STAMP brings us non-destructive single-cell profiling without the sequencing www.omic.ly/stamp-brings...
STAMP brings us non-destructive single-cell profiling without the sequencing
No sequencer needed: Imaging based single-cell multiomics
omic.ly
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
www.biorxiv.org/content/10.1...
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...
biorxiv.org
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...
Seminar Series – GESTALT – Global Alliance for Spatial Technologies
globalspatial.org
Awesome work by awesome people! Endless innovation by @lgmartelotto.bsky.social and team. Can’t wait to try it 💪
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...
cell.com
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...
St. Jude Research@stjuderesearch.bsky.social · last yr.“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 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)
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...
nature.com
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!
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...
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
academic.oup.com
#singlecell to #spatial converts .. means a lot more python than r… great tool to help transition academic.oup.com/bioinformati...
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
academic.oup.com
MCGAE: unraveling tumor invasion through integrated multimodal spatial transcriptomics #SingleCell 🧬🖥️ academic.oup.com/bib/article/...
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.
academic.oup.com
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. 🧪
Cellular atlases are unlocking the mysteries of the human body
Scientists reflect on insights from the Human Cell Atlas.
go.nature.com
Cool tool for segmentation free #spatial #transcriptomics onlinelibrary.wiley.com/doi/10.1002/...
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....
onlinelibrary.wiley.com
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...
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 ...
biorxiv.org
#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
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
github.com
🚀 Ready to learn about Spatial Omics? Learn from @stemang.bsky.social & @lgmartelotto.bsky.social in this hands-on R/Bioconductor course! Master imaging vs. sequencing methods, experimental design & tidy data principles for cutting-edge spatial omics analysis www.physalia-courses.org/courses-work...
