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G4X-viewer

g4x-viewer.singulargenomics.com

Explore G4X-data

G4X Viewer


G4X-viewer is an open-source, browser-based application for interactive visualization of G4X-data. Explore tissue images, transcripts, and segmented cells, adjust layer visibility, filter cells, and capture screenshots of features of interest. The available layers depend on the data included in your sample.

Use regions of interest (ROIs) to compare selected areas of your sample in the dashboard and export data for further analysis. Transcript display controls let you adjust how many transcripts are rendered while exploring large datasets.

Use the hosted application, or run the same web application locally using the instructions in the GitHub repository.

Data compatibility

G4X-viewer v4 uses the g4x-viewer.zarr store. For older datasets that use separate viewer files, use the legacy viewer, or use G4X-helpers migrate to convert supported legacy data and generate a v4-compatible viewer store.


viewer

Start with the viewer guide to learn how to load your sample and use the controls for each data layer.

The viewer pages include:

  • loading source data
  • on-screen controls
  • protein layer controls
  • fH&E layer controls
  • transcript layer controls
  • segmentation layer controls
  • UMAP cell filter
  • flow cytometry cell filter


dashboard

Use the dashboard guide to compare transcript, cell, and protein information across selected ROIs. The viewer and dashboard share the same session, so you can switch between spatial exploration and ROI comparisons. Available plots depend on the data in your sample.

The dashboard pages include:

  • ROI selection guide
  • expression box charts
  • pie charts
  • expression bar charts
  • heatmap charts


resources

See resources for video tutorials and introductory slides. Some resources demonstrate earlier viewer versions, so controls and supported data formats may differ from v4.


support

Got feedback or ideas for additional tutorials?
drop us a note at care@singulargenomics.com.

Found a bug or want to report another problem regarding G4X-viewer?
please file a new issue on the G4X-viewer issue tracker

Want to get involved and add new features?
check out how to contribute.


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