Loupe Browser

From data to biological insights

Loupe Browser is a powerful visualization software that provides intuitive analysis functionality you need to explore your 10x Genomics data. This easy-to-use desktop application for Windows and MacOS is available at no cost, enabling anyone to uncover biological insights from their data.

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Download Loupe V(D)J
Loupe Browser

Help shape the future of data visualization

Have you used Loupe Browser in your analysis and visualization of single cell or spatially resolved datasets? Do you plan to use it in the future? Share your feedback and feature wish list by filling out this 5-minute survey.

  • Multidimensional analysis

    Interrogate different molecular readouts, within and across samples, to drive discovery.

  • Analysis with simple clicks

    Explore data with this user-friendly interface to deepen your biological understanding.

  • Expert support

    Leverage comprehensive software videos, tutorials, and more to accelerate your analysis.

Single Cell Gene Expression

Characterize cellular heterogeneity

Explore the cellular composition in complex biology, uncover new cell subsets, and perform comparative analysis to uncover changes in cell populations across samples.
  • Loupe Browser gene/feature expression, represented as t-SNE, list, and violin plots

    Examine gene expression patterns

    Visualize expression profiles and differentially expressed genes across cell clusters.
  • Loupe Browser cell type clusters, represented as t-SNE, list, and heatmap

    Explore cell type compositions

    Examine and refine cell clusters to identify new or rare cell types.
  • Loupe Browser gene/feature expression data—shown as antibody t-SNE, list & graph-based table of upregulated genes per cluster

    Discover multiomic insights

    Utilize single cell gene and protein expression data to comprehensively profile new cell states.
  • Loupe Browser side-by-side view of cell type clustering data from two different samples

    Compare across samples

    Uncover differences in expression patterns, cell types, and their abundance.
Single Cell Immune Profiling

Gain a multiomic view of the immune response

Interactively explore immune complexity across multiple samples and cell types to understand gene usage, repertoire diversity, clonal expansions, and more.

  • Overlay gene expression and V(D)J data

    • Annotate immune cell subtypes by overlaying clonotype information onto gene expression profiles.
    • Visually explore links between phenotype and clonotype information by overlaying cell surface protein data.
    Loupe Browser displaying cell type clustering t-SNE overlaid with clonotype data

  • Explore the immune repertoire

    For our Single Cell Immune Profiling product, we provide an additional visualization software, Loupe V(D)J Browser, for more in-depth analysis of data.
    • Evaluate clonotype frequency, V(D)J gene usage, and pairing distribution to characterize T- and B-cell repertoire.
    • Visualize and compare key repertoire metrics across cell types and samples.
    Loupe VDJ Browser data with V-J gene heatmap and list
Single Cell Multiome ATAC + Gene Expression

Unify epigenomic and transcriptomic insights

  • Uncover multiomic markers for cell-type classification.
  • Refine cell types and states using simultaneous chromatin accessibility and gene expression measurements from the same single cells.
  • Investigate gene regulatory linkages between open chromatin peaks and gene expression.
Loupe VDJ Browser data with graphs representing linkages between chromatin peaks and gene expression data
Spatial Gene Expression

Visualize tissue transcriptomics

  • Analyze gene expression patterns to determine cell types and their localization within a tissue section.
  • Perform differential gene expression analysis across regions of interest.
  • Overlay gene expression, and protein expression onto tissue morphology.
  • Download Loupe Browser
  • Explore tutorials
Loupe Browser tissue image overlaid with Visium spot data, including cell clusters & up-regulated genes per cluster
Other Supported Analyses and Visualizations

Loupe Browser enables data analysis for many single cell applications

  • Epigenetics

    Explore Single Cell ATAC data in Loupe Browser to perform differential chromatin accessibility analysis, find cell clusters enriched for transcription factor motifs of interest, and compare open chromatin profiles across samples.

  • Barcode Enabled Antigen Mapping

    Screen the binding specificities of multiple antigens or epitopes for B or T cells using Single Cell 5’ Barcode Enabled Antigen Mapping. Obtain the corresponding paired, full-length receptor sequences for downstream expression and functional testing.

  • Multiomic Cytometry

    Visualize and interpret results from your Multiomic Cytometry experiment for more robust cell-type identification using both cell surface proteins and gene expression readouts.

  • CRISPR Screening

    Visualize data from Single Cell CRISPR Screening to characterize CRISPR perturbation phenotypes across guide targets and assess knockdown efficacy.

Frequently Asked Questions

Loupe Browser supports the analysis of data from the following products:

Loupe V(D)J Browser is a separate visualization software application that provides specific functionality to analyze TCR and BCR clonotype information from the Single Cell Immune Profiling product.

Loupe Browser is a point-and-click software that enables anyone, no matter their level of bioinformatics expertise, to analyze 10x Genomics data.

Loupe Browser uses a .loupe file to visualize 10x Genomics data. The .loupe file is generated by downloading and running the compatible 10x Genomics Analysis Software (see 10x Genomics Cloud Analysis for options to run software quickly and easily), which processes raw data into standard file formats that can be used for downstream interpretation. Once you have generated the Analysis Software output you can download the latest version of Loupe Browser and start to analyze your data.

The following resources are available to help you analyze data with Loupe Browser:

Loupe Browser is available at no cost to anyone analyzing 10x Genomics data.

Explore documentation, tutorials and datasets for each product on our support site

Get Started with Loupe Browser