Skip to content

What are Tissue Wand Parameters?

Tissue Wand Parameters: Parameters used by the Tissue Wand tool to control raster image sampling, luminance thresholding, and contour extraction for automated tissue boundary detection.

  • Layer: Select a raster layer on the map for tissue boundary detection.

    Available Layer Types

    The tissue wand only works for raster layers (e.g. Background histology images or Factor layers set to RASTER mode). Vector layers (cells, hexagons, genes) cannot be sampled.

  • Extent: Define the spatial scope and area used for sampling and tissue boundary detection.

    Option Definition
    View Samples the current visible map viewport. Best for high-zoom anatomical subregions.
    Layer Samples the complete raster layer across the entire slide footprint.
    Island Interactively detects and outlines only the specific connected tissue section or island clicked on the map canvas.

  • Stain: Specify the microscopy staining modality to determine optical contrast between tissue and background.

    Option Definition
    H&E Brightfield light microscopy mode where stained tissue absorbs light and appears darker than the bright slide glass.
    Fluor Fluorescence dark microscopy mode where stained tissue emits bright fluorescent signal against a dark background.

  • Tolerance [Numeric (0–255)]: Grayscale luminance cutoff threshold separating tissue pixels from background. Higher values in H&E include lighter tissue; higher values in Fluor select only high-intensity signal.

  • Min Area [Numeric (px)]: Minimum pixel area threshold. Contours smaller than this value are discarded to filter out dust, background noise, and small debris.
  • Anti-alias: If checked, applies contour smoothing (d3-contour) to yield natural, smooth biological tissue margins.
  • Contiguous: If checked, retains only the single largest continuous tissue block in the sampled area, discarding detached satellite fragments.
  • Invert: If checked, inverts classification polarity, treating bright regions as tissue in H&E or dark regions as tissue in Fluor.

Related Pages

Concepts

Manual Pages

How-to Guides