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Loupe Browser 6.2.0 (Jul 18, 2022)

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Release notes

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.

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.

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.

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.

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.

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.

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.

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.