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Stage 1 - Detection

In this stage, Cellogram detects the markers in the image. There are options for helping out the detection algorithm.

  • Sigma

    Determines size of Gaussian for fitting to the markers in the image. If too many markers are detected, Sigma should be increased.

  • Otsu

    Cellogram generates a binary mask of the image at the Otsu-threshold level. However, this level is scaled with the factor entered here. If markers in dark regions are missed in the detection, lower this value.

  • Detect

    Initiates detection

  • Histogram (graph)

    Histogram of pixel intensities in the image. Green bars left and right indicate the minimum and maximum value displayed.

  • min (slider)

    Adjust the minimum pixel intensity displayed to stretch contrast in the image. This aids manual detection only.

  • max (slider)

    Adjust the maximum pixel intensity displayed to stretch contrast in the image. This aids manual detection only.

  • Advanced vertex options

    • Delete (icon)

      Activates deleting of incorrectly detected markers by clicking on them with the red crosshair. Hotkey is d. Deactivate by clicking on the Delete button again.

    • Add (icon)

      Activates adding of undetected markers by clicking on them with the green crosshair. Hotkey is a. Deactivate by clicking on the Add button again.

    • Move (icon)

      Move a vertex to a new position by dragging

  • Back (icon)

    Removes image and detected points

  • Next (icon)

    Advance to Stage 2 - Meshing by finding the mesh connectivity