Segmentation

During the segmentation process, up to 10 different methods can be used in parallel in order to segment the rejected particle. Each method consists of specific filters (1-5) or user-defined macros (6-10) which are applied on a transient version of the image surrounding the current particle. Note that if the resulting image is not already thresholded, the final binary mask will be generated

Options: Sets the options related to the segmentation process.

Min Part. [n]: Sets the minimal number of particles expected after segmentation. Default setting is 1.

Max Iter. [n]: Sets the maximal number of iterations a particle and resulting segmented particles can undergo the segmentation process. Default setting is 2.

Debugging Mode: If checked, MicrobeJ will create, for every segmented particle, a stack of images that show the resulting binary mask for each selected method.

Methods: Selects the methods used by the segmentation process.

Auto:  If checked, a set of default methods will be used to segment the rejected particles. If not checked, allows the user define the methods to be used.

Filter: Allows any of the different filters to be applied to the image surrounding the particle before auto-thresholding. Five filters are available: none, Shape Index, Sharpen, Watershed and Watershed irregular structures.

None: No filter will be applied to the particle image processor before auto-thresholding.

Shape Index: Converts the particle image processor into a shape index map before auto-thresholding (see Fiji documentation for more details).

Sharpen: Increases contrast and accentuates detail in the particle image processor using a sharpen filter (see ImageJ documentation for more details).

Watershed: Uses a standard Watershed segmentation algorithm on the particle binary mask (see ImageJ documentation for more details).

Watershed irregular: Uses a Watershed segmentation algorithm on the particle binary mask (see Biovoxxel Tool box documention for more details).

Method: Allows any of the different automatic thresholding methods to be selected (see Fiji Auto_Threshold manuals for more details). The Default method is the modified IsoData algorithm used by ImageJ. Note that the threshold levels will be calculated using pixels values measured inside the particle boundary.

Macro: Sets the functions to be applied on the image surrounding the current particle image using the ImageJ macro code (see Intro to Macro Programming for more details).

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