Download for Windows

Download for MacOS

Improved image export with high resolution.

View per-codeword localization for custom and boosted genes in Xenium Prime 5K data.

Xenium Explorer 3.2.0 highlights

Xenium Explorer

Download Xenium Explorer

Fixed a bug that caused custom cell groups to be lost after closing Xenium Explorer.

Xenium Explorer 3.1.1 highlights

New scaled transcript view to visualize spatial transcript distribution for highly and lowly expressed genes at any zoom level.

Sorting of transcripts and cells in Selections window.

Xenium Explorer 3.0.0 highlights

Supports the visualization of multimodal cell segmentation, including coloring cells by segmentation method.

Customize colors across images, cells, and transcripts with a custom hex# color selector.

Supports the import, alignment, and visualization of immunofluorescence (IF) images with >6 channels.

Xenium Explorer 2.0.0 highlights

Align and explore an immunofluorescence image from the same section directly on the Xenium data.

Adjust, add, or download and share keypoints after the image alignment workflow is completed.

Import up to two post-Xenium images per sample.

Xenium Explorer 1.3.0 highlights

Align and explore an H&E image from the same section directly on the Xenium data.

Import a CSV file and view clustering results from community-developed tools.

Use the lasso tool to export Cell IDs for further analysis in community-developed tools.

Streamline files for Xenium Explorer visualization - Z-stack morphology.ome.tif image is now optional.

Xenium Explorer 1.2.0 highlights

Explore Xenium image-based in situ data with intuitive controls.

Organize markers of interest and visualize 3D localized transcripts at any scale.

Examine segmented cells colored by transcript density or clustering result.

Compare gene expression profiles and cell type proportions across tissue regions with a versatile lasso tool.

New: Save imported gene groups across sessions with Saved Views.

New: Compatible with all Xenium Onboard Analysis versions, but required for v1.3+.

Xenium Explorer 1.1.0 highlights

Xenium Explorer 1.0.0 highlights

Explore Xenium In Situ data from the tissue scale down to subcellular resolution with our interactive visualization tool.

Overview

Download Center

Getting Started

Xenium Explorer Demos

Tutorials

Release Notes

Xenium Onboard Analysis

Xenium Ranger

Xenium Panel Designer

Analysis Guides

List of Xenium Explorer-compatible input files.

Xenium Explorer Inputs

Learn about Xenium Explorer and orient yourself to its interface and features.

Navigate Xenium Explorer

Image Layer

Cells Layer

Learn how to interact with transcript data.

Transcripts Layer

Find tips for examining cell segmentation, cell cluster assignment, and gene expression with Xenium Explorer.

Check Data Quality

Use Xenium Explorer lasso tools to narrow your focus to the cells that matter.

Export Regions of Interest

Save UI settings, transfer configurations to another window, and share settings with others.

Save and Share

Align post-Xenium images or import images aligned with third-party tools.

Image Alignment

Convert post-Xenium images to a format compatible with Xenium Explorer.

Converting Images

Introduction

Learn about Xenium Explorer and get oriented to its interface and features.

Interface and Features

Explore Xenium In Situ data, from tissue macrostructures to subcellular resolution, with our interactive visualization tool. Pinpoint the locations of specific transcripts, check cell segmentation, and inform downstream analysis.

What is Xenium Explorer?

Walk through Xenium Explorer features for investigating your in situ gene expression data.

Getting Started with Xenium Explorer

New to Xenium Explorer?

View the latest updates to Xenium Explorer.

Learn more about Xenium In Situ instrument analysis software.

Reanalyze data from Xenium In Situ solutions.

Browse Q&As from the 10x Genomics support team.

Access free, publicly available data generated with Xenium In Situ Gene Expression solutions.

Datasets

A collection of introductions, tutorials, and blogs for data analysis beyond 10x Genomics software.