<LinkableSection id={"v-5-0-0"} title={"v5.0.0 (October 5, 2026)"}>

_This is the initial release of 10x Explorer. It builds on the capabilities of Xenium Explorer and adds new features (described below). Future in situ data visualization improvements will be added to 10x Explorer. Xenium Explorer ([latest version 4.1.1](/support/software/xenium-explorer/latest/release-notes/release-notes-for-XE)) will continue to be available for use, but is not in active development._

- Supports Atera Gene Expression and Xenium In Situ data visualization. 10x Explorer is [compatible](/support/software/tenx-explorer/latest/getting-started#sw-compat) with all Atera Onboard Analysis and Xenium Onboard Analysis versions.
- [Transcript Layer](/support/software/tenx-explorer/latest/tutorials/nav-transcripts) updates:
   - Updated user interface for selecting genes and creating custom gene groups in the app, which can be downloaded in CSV format. For CSV upload, the [custom gene group CSV format](/support/software/tenx-explorer/latest/tutorials/nav-transcripts#creating-gene-groups) includes new column options: "group_color" and "gene_color". Due to these updates, previously saved custom gene groups will not carry over from Xenium Explorer to 10x Explorer and will need to be re-uploaded.
   - View [transcript density](/support/software/tenx-explorer/latest/tutorials/nav-transcripts#transcript-density) bin colors by gene or gene group color.
   - Export [transcript localization gallery](/support/software/tenx-explorer/latest/tutorials/nav-transcripts#gallery) images as PNG files.
   - [Scaled transcript view](/support/software/xenium-explorer/latest/tutorials/nav-transcripts#scaled-transcripts) and the [per-codeword gallery](/support/software/xenium-explorer/latest/tutorials/nav-transcripts#per-cw-loc) are no longer supported in 10x Explorer.
- View cell color by custom cell metric values that are specified in a [custom cell metrics CSV file](/support/software/tenx-explorer/latest/tutorials/nav-cells#cell-metrics).
- [Annotate data](/support/software/tenx-explorer/latest/tutorials/nav-annotations#make-a-selection) with a circular selection shape, in addition to the rectangular and freehand options. In edit mode, annotation shapes can be moved with a new toggle.
- When [images are exported](/support/software/tenx-explorer/latest/tutorials/nav-ui#img-export) (both quick export and high resolution export), change the background to black (default), white, or transparent.
- In the Image Layer, the slider values are shown in arbitrary units (au) instead of photoelectrons (pe).
- General performance improvements.

</LinkableSection>

v5.0.0 (October 5, 2026)

Explore in situ data from the tissue scale down to subcellular resolution with our interactive visualization tool.

10x Explorer

Atera

Xenium

Gene Expression

Release Notes for 10x Explorer

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

Overview

Getting Started

Download Center

10x Explorer Demos

Tutorials

Release Notes

Analysis Guides

List of 10x Explorer-compatible input files.

10x Explorer Inputs

Learn about 10x Explorer and orient yourself to its user interface and features.

Navigate 10x Explorer

Find tips for examining cell segmentation, cell cluster assignment, and gene expression with 10x Explorer.

Check Data Quality

Learn how to interact with single and multichannel image data.

Image Layer

Learn how to interact with nucleus and cell segmentation, as well as cell cluster data.

Cells Layer

Learn how to interact with transcript data.

Transcripts Layer

Create or import annotations for your dataset and extract transcript, cell, and protein stats for regions of interest.

Annotation Layer

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

Save and Share

Set up and access Onboard Analysis files from AWS S3 bucket to visualize in 10x Explorer

Open Analysis Files from AWS

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

Image Alignment

Convert post-instrument images to a format compatible with 10x Explorer.

Converting Images

Learn about 10x Explorer inputs and data QC.

Introduction

Learn about 10x Explorer's interface and features.

Interface and Features

Learn about 10x Explorer image alignment features.

Explore Atera and 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 annotate regions of interest to inform downstream analysis.

What is 10x Explorer?

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

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