Thresholding

This sub-panel contains settings related to the auto-thresholding function. Press to display or hide the thresholded values on the active image. Press to open the thresholding options window. Note that the icon will turn green if any of the options (Image Treatment or Threshold Calculator) is activated.

Channel: Allows any of the four different channels (1-4) of the active image to be selected for the bacteria detection. Select “Binary” to use an existing binary mask instead of automatic thresholding.

Background type: Selects the type of background. Select “Dark”, if the image background is darker than the particles to be found (i.e. fluorescent images). Select “Bright”, if the Image background is brighter than the particles to be found (i.e. phase contrast images).

Enable Auto-threshold: This should be checked if the selected channel is not a binary mask. The default setting is checked.

Auto-threshold method: Allows any of the different automatic thresholding methods or any of the different local thresholding methods in ImageJ to be selected (see Fiji Auto_Threshold or Auto Local Threshold manuals for more details). The Default method is the modified IsoData algorithm used by ImageJ. The Local Default method uses the Default method on a “pseudo-flat field” corrected version of the image to be analyzed. The “pseudo-flat field” correction is accomplished by subtracting the Gaussian-blurred (kernel size: 40 pixels) image version of the image to be analyzed. The Region of Interest (ROI) Manager method loads the ROIs stored into the ROI Manager in place of actual particle detection.

Auto-threshold offset: Sets and adjusts an offset value to the minimum (dark background) or the maximum (bright background) threshold value. Default setting is 0.

Display Threshold : If toggled, the thresholded values will be displayed in yellow or hidden on the active image. Note that the local thresholding methods cannot be displayed on the active image. As such, the display threshold option will be disabled when a local thresholding method is selected.

Thresholding Options : Opens the thresholding options window. Note that the icon will turn green if any of the options (Image Treatment or Threshold Calculator) is activated.

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