Image

The background source is an image.

  • Method: Automatic
    The background is extracted from the image itself and subtracted from the source. A blur filter (Gaussian) is applied to the source image to generate the background representation.

    Blur diameter: The Gaussian filter will have a kernel size matching the blur diameter.
  • Method: Manual
    The background is an external image. It can be collected directly from the acquisition device or generated by a pipeline (e.g. applying to the source image a Mean/Median filter). The background image must be stored in a separate Image-Set.

Constant

The background source is a constant value.

  • Method Automatic:
    The background is computed using one of the Thresholder algorithms and subtracted from the source.
  • Thresholder: Mean
    Compute the background value as the mean of the plane or time points or full dataset and subtract it from the source image.
  • Thresholder: Histogram based
    Compute the background value applying one of the available algorithms (Auto, Huang, Li, Yen).
  • Mean computed as single value:
    • Over all the planes
    • Over all the Time Points
    • Over the full dataset (both checks on)
  • Method: Manual
    The background value is manually set to a specific value.
  • Maintain original color range

    The output of this operation might shift the intensity range and might thus be unrelated to the color range. This parameter selects whether or not this operation adapts the color range to meet the output.
  • Correction:

    Preserve Bright: This method will only preserve parts of the image that have higher intensity values than the background (e.g. bright parts in a grayscale image). After this method is finished, the background intensity will be zero and the remaining foreground pixels will have a higher intensity value.
    Preserve Dark: This method will only preserve parts of the image that have smaller intensity values than the background (e.g. dark parts in a grayscale image). This method will invert the intensity of the image, so that foreground pixels will again have a higher intensity value. After this method is finished, the background intensity will be zero and the remaining foreground pixels will have a higher intensity.
    Preserve Both: This method tries to preserve both brighter and darker parts of the image. Therefore, an average background intensity value will be calculated over all time points first. After this method is finished, the background intensity will be shifted to this calculated value. Formerly darker parts will still be darker than the background and formerly brighter parts will be brighter than the background.