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segmentation layer


This section describes how to customize cell segmentation displays, adjust mask appearance, and apply cell-level filtering based on clustering, protein expression, transcript abundance, and other analysis outputs.

reference image

segmentation layer controls


These controls select segmentation and cluster sources, style cell masks, and apply cell-level filters.

features

  • Segmentation Source:

    Selects which segmentation source is displayed in the viewer. By default, the viewer provides nuclear expansion segmentation. You can use the g4x-helpers toolkit to apply additional segmentations that appear in this drop-down menu.

  • Cluster Source:

    Selects which clustering annotation is displayed in the viewer. By default, the viewer provides base Leiden clustering. You can use the g4x-helpers toolkit to upload additional cluster annotation layers that appear in this drop-down menu.

  • Cell Fill Opacity:

    Adjusts the transparency of cell fills when enabled. A value of 0 is fully transparent, while 100 is fully opaque.

  • Cell Boundary Toggle:

    Shows or hides cell boundaries, which are displayed as fully opaque lines. This toggle triggers a warning because displaying boundaries for large datasets can be resource intensive and may cause browser instability or crashes.

  • Boundary Line Weight:

    Adjusts the thickness of displayed cell boundary lines.

  • Enable Cluster Filter:

    Enables or disables the filter specified in the Cluster Filter Settings section.

  • Display Filtered Cells:

    Shows or hides cells excluded by the active filter. When shown, excluded cells appear as gray polygons in the cell mask layer. This option is available only when a filter is actively applied to the image.

  • Cluster Filter Settings:

    These features specify the filter state for cell mask overlays. They rely on clustering information and expression of protein or RNA species of interest. Clusters labeled -1 were not assigned to a cluster, typically due to filtering or quality-control processes in onboard analysis.

    • Apply Filter: Applies the current filter to the displayed image.
    • Clear Filter: Clears the current filter from the displayed image.
    • Search Clusters: Searches clusters by name. Manually updated cluster names can represent cell types or other annotations.
    • Export Colormap: Exports the displayed cluster and color data.
    • Advanced Filter: Opens additional options for filtering the cluster table.
    • Toggle All: Toggles selection of all clusters on or off.
    • Toggle Cluster: Toggles selection for a single cluster.
    • Show Selected: Hides all non-selected clusters.
    • Change Channel Color: Changes the color selection for a given cluster.
    • Change Page: Moves between pages when there are too many clusters to display at once.

  • Import/Export Colormap:

    Import or export the cluster colormap as a JSON configuration file.

    • Import: Click Import, then select a previously saved JSON configuration file.
    • Export: Configure the cluster colors as desired, then click Export and choose a save location and filename.

  • UMAP Filter:

    Opens the UMAP filtering interface, allowing you to select cell populations based on their position within the UMAP embedding.

    See UMAP filter for additional details.

  • Flow Cytometry Filter:

    Opens the flow cytometry filtering interface, allowing you to select cell populations based on protein expression distributions.

    See flow cytometry filter for additional details.



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