Welcome to The Readout! Each quarter, we’ll share a selection of highlights, updates, and resources for innovative investigators like you. Let’s jump right in — and happy reading.

What's new: plate-based GEM-X Flex — the next step up in scalability

The plate-based GEM-X Flex is revolutionizing single cell genomics, putting breakthrough technology within reach for big projects and population-scale studies. Designed to dramatically reduce the cost per cell, this system is your solution for high-throughput discovery. The advanced chemistry allows for 384-barcoding, letting you process up to 8 million cells per chip. This unprecedented capacity, combined with a streamlined plate workflow, minimizes hands-on time, reduces errors, and ensures exceptional reproducibility across hundreds of samples. Unleash the power of massively-scaled single cell data you can trust.

Learn how the new plate-based GEM-X Flex redefines high-throughput single cell experiments.

Publication highlight

Comparison of single-cell RNA-seq methods to enable transcriptome profiling of neutrophils in clinical samples

In their publication Hatje et al. (2025)¹, compared three commercially available single-cell RNA sequencing (scRNA-seq) technologies for their suitability in profiling neutrophils from clinical samples, a notoriously difficult cell type due to low RNA content and high sensitivity. They came to the conclusion that the GEM-X Flex workflow was the best choice for implementation in clinical trials due to its superior concordance with flow cytometry and a practical sample collection protocol that supports stabilization at clinical sites prior to transport. The study establishes crucial guidelines for prompt sample processing (fixation within 2 hours) to ensure the integrity of the sensitive neutrophil transcriptome.

¹Hatje, Klas, et al. "Comparison of single-cell RNA-seq methods to enable transcriptome profiling of neutrophils in clinical samples." Cell Reports Methods 5.9 (2025).

Your data & discovery center

Analysis Guides

Analysis of 10x Genomics data is full of possibilities. Here is a collection of introductions, tutorials, and blogs for data analysis beyond software developed by 10x Genomics. We hope that our updated analysis guides will help you navigate your exciting analysis journey. 
Additionally, we also recently shared an overview on how to include pathology annotation in Xenium Explorer.

On-demand webinars

Watch our recent webinars on-demand

• Educational Xenium webinar series
  
  • Xenium Panel Design
  • Xenium Workflow
  • Xenium Data Analysis
• Xenium for drug development: Analyzing cancer survivors, profiling lead compounds 
• Xenium In Situ: Plateforme d’imagerie spatiale unicellulaire [in French]
• Educational webinar Visium HD 3': Deeper spatial discovery

Stay in the loop! Did you know we have a newsletter just for technology updates? Sign up and choose Product Updates, Technical Workflow Updates, and Technical Software Updates to get the latest news delivered straight to your inbox.

Latest product releases

Xenium Analyzer 4.0 with Xenium Onboard Analysis v4.0.1

Dorsal root ganglion tissue dataset provided by researchers in Dr. Theodore Price’s laboratory at the University of Texas at Dallas

Our recently released Xenium Analyzer 4.0 and updated Xenium Onboard Analysis v4.0.1 introduces support for the Xenium Gene & Protein Expression assay. Key features include:

• Protein subpanel selection: Users can now choose specific protein subpanels for analysis. Enhanced image processing: Improved cell segmentation and nucleus detection algorithms provide more accurate results.
• Background subtraction: Advanced techniques account for tissue autofluorescence, improving protein quantification.
• Secondary Analysis: Cells with fewer than five transcripts are excluded from downstream analysis for higher data quality.
• Updated Outputs: New file naming conventions and additional QC metrics enhance data interpretation.

This update is essential for researchers using the Xenium platform, offering improved functionality and analysis capabilities.

More Xenium In Situ updates

Xenium In Situ Gene and Protein Expression data for FFPE Human Renal Cell Carcinoma

Take your findings from transcript to function with an optimized and automated workflow using Xenium Protein subpanels, and unlock a new world of immunology and oncology insights with integrated gene and protein expression.

Cells from human pancreas with improved cell boundaries between adjacent cells

Also available is the new multimodal approach that takes advantage of cell boundary, interior, and nuclear staining to allow for improved cell calling and enables more confidence in cell segmentation than ever before. Explore deeper with 5,000-plex gene panels for unparalleled spatial discovery power.

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Visium Spatial updates

Visium HD 3' Gene Expression for FF Human Mouse Xenograft

Expand your spatial discovery potential and experimental flexibility with a 3’ poly(A)-based Visium HD assay. The Visium HD 3’ assay powers whole transcriptome spatial gene expression at single cell scale across fresh frozen tissues from any species and enables feasibility for isoform, BCR/TCR, and SNV detection.

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