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Previous Versions

Previous Versions

Loupe Browser 8.0.0 (Mar 25, 2024)

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Loupe Browser 8.0.0 highlights

  • Enter the era of whole transcriptome analysis at high definition: Loupe Browser 8 supports manual alignment, visualization and analysis of Visium HD!
  • Explore the relationships between cell types or pathways with the new co-expression functionality.
  • Analyzing a large dataset? No problem. Loupe Browser 8 enables differential expression and reclustering analysis for unlimited barcodes or bins.
Release notes

Loupe Browser 7.0.1 (Oct 12, 2023)

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Loupe Browser 7.0.1 highlights

  • It’s a whole new Loupe Browser! New user interface enables faster data analysis through easy feature discovery and in-app descriptions of analysis options.
  • Analyze Seurat processed data without coding. Use the LoupeR package to convert your Seurat object to a CLOUPE file and analyze in Loupe v7.0 onward.
  • Find genes of interest across experimental conditions using the new Multi-sample Differential Expression feature.
  • (Loupe v7.0.1) Addresses bugs for macOS Catalina and Big Sur, Peak View for Multiome data, and improves user interface.
Release notes

Loupe Browser 6.5.0 (May 12, 2023)

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Loupe Browser 6.5.0 highlights

  • Visualize and analyze Visium Protein Expression! Antibody list automatically populated under the Active Feature List tab, and updated user interface enables easy barcode selection.
  • Perform cell typing analysis of Reference Free Deconvolution results through the new Spot Deconvolution feature! Files must be generated using Space Ranger v2.1 or later.
  • Export Heatmap as high resolution SVG files.
  • Bug fixes and general improvements, including deleting reclustering results and changing spot opacity in the Visium manual aligner.
Release notes

Loupe Browser 6.4.1 (Jan 18, 2023)

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Loupe Browser 6.4.1 highlights

  • Improved interactivity with V(D)J and BEAM datasets including new user interface for assigning categories to clonotypes.
  • The BEAM antigen list in the Active Feature List dropdown menu is pre-populated to make it more easily accessible.
  • The ability to filter BEAM datasets by antigen specificity score.
  • 6.4.1 specific: Fixed a bug in Visium manual aligner to allow display of larger image files.
Release notes

Loupe Browser 6.3.0 (Sep 22, 2022)

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Loupe Browser 6.3.0 highlights

  • Projections can be exported as vector SVG files, providing a higher resolution image to use for presentations and publications.
  • Filtering and reclustering is now available for Visium datasets! This feature enables reclustering of Visium data for clusters or regions of interest to identity new insights.
Release notes

Loupe Browser 6.2.0 (Jul 18, 2022)

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Loupe Browser 6.2.0 highlights

  • New CytAssist Image Aligner enables image alignment using landmark selection between a CytAssist generated image and a microscope image of the same tissue section on a plain glass slide.
  • New functionalities to Fiducial Aligner workflow include support for QPTIFF format and ability to name immunofluorescence channels which are displayed in Space Ranger generated output files.
  • Reclustering for Gene Expression (GEX) data in GEX + Antibody Capture, GEX + CRISPR Guide Capture, and GEX + ATAC datasets is now available.
Release notes

Loupe Browser 6.1.0 (Apr 29, 2022)

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Loupe Browser 6.1.0 highlights

  • A major redesign of the Visium Manual Aligner enables faster and more accurate fiducial and tissue detection, including automated brightness and contrast leveling, zooming, and new keyboard shortcuts.
  • Feature Barcode lists are more easily accessible to rapidly explore protein and CRISPR data.
  • The embedded Spatial Tutorial dataset now allows the exploration of the spatial enrichment (Moran’s I) feature.
Release notes

Loupe Browser 6.0.0 (Oct 7, 2021)

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Loupe Browser 6.0.0 highlights

  • The Loupe rendering methods have been reworked to enable faster visualization, interaction, and analysis of datasets of 1 million+ cells.
  • Differential expression has 4x faster calculation speeds and support for up to 1 million cell datasets.
  • The export of projection coordinates as a CSV is now supported, including for newly generated tSNE and UMAP projections via the Filtering and Reclustering Wizard for Single Cell Gene Expression datasets.
Release notes

Loupe Browser 5.1.0 (Jun 16, 2021)

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Loupe Browser 5.1.0 highlights

  • Reclustering workflow now supports generating a UMAP projection in addition to the t-SNE projection.
  • Visium Image Manual Aligner now includes additional support for images with difficult to detect fiducials.
  • A new Spatial Enrichment table which allows users to sort and filter features by their Moran’s I value for Visium Spatial Gene Expression is added.
Release notes

Loupe Browser 5.0.1 (Feb 3, 2021)

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Loupe Browser 5.0.1 highlights

  • Introduces support for VDJ clonotypes created with Cell Ranger 5.0 and above. Previous versions of Loupe Browser may be used to explore VDJ data generated by Cell Ranger 4.0 and earlier.
  • For .vloupe files, updates include improved performance of the clonotype table for larger datasets and iNKT/MAIT filtering options.
  • Introduces filtering and reclustering for single-cell gene expression datasets.
Release Notes

Loupe Browser 4.2.0 (Sep 9, 2020)

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Loupe Browser 4.2.0 highlights

  • Introduces support for Single Cell Multiome ATAC + Gene Expression assay and Cell Ranger ARC 1.0 pipeline.
  • Should be used to explore VDJ data generated by Cell Ranger 4.0 and earlier.
Release notes

Loupe Browser 4.1.0 (Jun 23, 2020)

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Loupe Browser 4.1.0 highlights

  • Introduces linked windows to provide concurrent views of the same dataset, log normalization, and violin plots.
  • Supports the processing, manual alignment and visualization of immunofluorescent Visium data.
Release notes

Loupe Browser 4.0.0 (Dec 2, 2019)

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Loupe Browser 4.0.0 highlights

  • Enables support for Visium Space Gene Expression datasets and CLOUPE files generated by Space Ranger 1.0.
  • Introduces the Visium Manual Alignment Wizard which allows users to line up the microscope image with a slide layout file, and to precisely label tissue for processing by the Space Ranger pipeline.
Release notes

Loupe Browser 3.1.1 (Jul 24, 2019)

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Loupe Browser 3.1.1 highlights

  • New filtering tab for creating and sharing complex boolean filters.
  • Multi-window mode makes it easy to have different views of the same dataset open in separate browser windows.
  • Newly enabled features for projections, including projection importing.
Release notes

Loupe Browser 3.0.1 (Nov 19, 2018)

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Loupe Browser 3.0.1 highlights

  • Explore new Feature Barcoding datasets.
  • ATAC dataset support, including new ATAC-specific features like the peak viewer.
  • Two new views added: feature plot view allows graphing by one or two features at a time, and split view segments projections by a specific cluster set.
Release notes