Visium Analysis

A whole new visual canvas to discover your spatial data

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Loupe Browser image

Your journey to whole transcriptome spatial insights

Our Visium Spatial Software Suite allows you to analyze and visualize spatial gene and protein expression data produced by the Visium Platform, even without bioinformatics help.

Visium analysis spatial
Space Ranger analysis pipelines

Translate sequencing data into gene expression-aligned images

Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images.

Align reads and process data with Space Ranger

Process Visium Spatial Gene Expression (GEX) and Protein Expression (PEX) data with brightfield and fluorescence images to align reads, generate feature-barcode matrices, and perform secondary analysis including clustering and differential gene expression.

Space ranger pipelines
Loupe Browser

10 ways to explore your spatial gene expression data with Loupe Browser

Loupe Browser allows you to interactively visualize spatial data from Space Ranger output.

1

Explore gene expression clusters in the tissue context

2

Map the expression of thousands of genes onto your microscope H&E or IF image

3

Identify gene signatures of neighboring regions

4

Annotate your tissue based on morphology

5

Define cell types with automated spot deconvolution

Space Ranger performs reference-free spot deconvolution to enable out-of-the-box cell type level analysis in Loupe.

6

Find spatially variable genes in a few clicks 

Space Ranger identifies genes with unique spatial patterns, which can be visualized in Loupe for new target gene discovery.

7

Dive deeper into regions of interest

8

Characterize immune cells with protein co-detection

The Visium Gene and Protein detection kit enables characterization of immune cells in distinct tissues with user friendly protein thresholding in Loupe.

9

Select tissue regions by gene or protein thresholds

10

Create high-quality figures for publications

Loupe Browser makes it easy to generate SVG and PNG formatted images to share in presentations or publications.

Discover spatial data

Explore diverse 10x Genomics datasets with various assays, samples, and species.

Visium Spatial family

Visium Spatial Platform

The Visium platform enables unbiased molecular profiling of frozen and fixed tissue sections, simple tissue handling, sensitive gene detection, and user-friendly software for visualizing gene expression.

Start your Visium journey