Mark objects

Purpose

Use the Mark Objects tool to mark detected objects automatically within the entire image or within regions of interest.

This detection algorithm is based on the current image adjustments histogram, not the raw image data.

Procedure

  1. Open an image and zoom to an area containing objects representative of the objects you wish to mark.
  2. Select a marker.
  3. In the Main window, go to the Pipelines ribbon and click Mark objects.

  4. In the Mark Detected Objects window, under Detection Space, choose either Use Full Image or Use Region(s) of Interest.

    If you choose Use Region(s) of Interest:

    • Click Use Existing ROIs to use existing contours.

      • Click a contour to select it; hold down Shift and click on contours to select multiple contours.
      • Click Done Selecting when satisfied with your selection.

    • Click Draw ROIs to trace a contour.

      • Trace a contour in the Tracing window.

      • Click Finished ROIs.

  5. Click a representative object—Stereo Investigator Cleared Tissue Edition software displays a preview of outlined detected objects.

    The representative object can be located outside of the region of interest, however, only objects within the region of interest will be marked.

    • For a list of contour measurements, click Contour Measurements . Stereo Investigator Cleared Tissue Edition software displays the results in the Contour Measurements window.
    • To use presets : See Presets section below the procedure.

  6. Adjust any of the parameters; every time you adjust a parameter, Stereo Investigator Cleared Tissue Edition software updates the Results.

    • Sensitivity: The higher the sensitivity, the smaller the detected object around the representative sample color (displayed under Object Color ).
      • Click Apply to refresh the preview.
      • To sample a different color, click on another color in the tissue.
    • Outline Point Density: Unavailable for this command.
    • Exclude objects: Excludes objects from detection that are Smaller than/ Larger than the specified area (type a value into the box); use in conjunction with the sensitivity setting.
      • Use Quick Measure Size for a quick estimation of the size of objects approximately circular.
    • Separate Objects: Check the box By Average Size and type the area in µm2 into the box. This may increase the accuracy for the count of detected objects.
    • Screen Edge Restrictions: Stereo Investigator Cleared Tissue Edition software ignores objects that meet the criteria you select by checking the boxes.
  7. Click Mark Objects to apply the parameters.

About Presets

Use presets in order to apply the same parameters to multiple images.

You can save and edit presets, and load previously saved presets.

Saving or deleting presets

  1. Click Presets and select Edit Presets.
  2. In the Save/Update dialog box, do one of the following:
    • Type a name for the preset, and click Save.
    • Select an existing preset and click Delete to remove it.

Loading an existing preset

  • Click Presets and select a preset from the list.

See Cell detection workflow, Outline objects