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source files


This section describes how to load G4X data into the viewer and manage layer visibility using the available layer controls.

reference image

source file controls


These controls cover data loading, Z-plane navigation, scale adjustment, and layer visibility.

features

  • Cloud Upload:

    Use this button to paste a cloud storage link and stream data into the viewer in real time.

  • Local Upload:

    Use this button to upload files from local storage. Depending on the viewer version, you can:

    • Upload a single Zarr file (available beginning with version 4.0.0), or
    • Upload multiple files directly from the g4x_viewer output directory generated by the G4X pipeline.

    When using legacy data and viewer versions, each file contains a specific data layer or metadata component of the G4X assay:

    • <sample_id>.ome.tiff — Contains all protein images stored as a composite image.
    • <sample_id>_HE.ome.tiff — Contains the fH&E image.
    • <sample_id>.bin — Contains segmentation mask vertices.
    • <sample_id>.tar — Contains transcript locations.
    • <sample_id>_run_metadata.json — Contains sample and run metadata.

    For additional information about viewer-compatible output files, see the g4x_viewer output documentation.

  • Image Size/Layer:

    Displays the current layer, total layer count, and image dimensions.

  • Manual Scaling:

    Controls the zoom level by setting the scale bar to represent a specific value. During standard zooming, the scale bar automatically updates as you zoom in and out of the image.

  • Overview Toggle:

    Shows or hides the image overview in the lower-left corner of the screen. This window displays the full image as a thumbnail, with the current viewing area outlined in red to help you track your position while zoomed in.

  • Layer Toggles:

    Shows or hides image layers displayed in the viewer.

    • Channel Settings: Shows or hides protein image layers.
    • Brightfield Images Settings: Shows or hides the fH&E layer.
    • Transcript Layer Settings: Shows or hides transcript dots.
    • Segmentation Layer Settings: Shows or hides cell segmentation masks.



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