Options

Thresholding: This panel contains parameters specifically related to the thresholding of the selected image.

Use Roi: If checked, the histogram used to compute the threshold value is performed on the current rectangular selection. If not, the histogram is performed on the entire image. Default setting is checked.

Stack Histo.: If checked, MicrobeJ will first compute the histogram of the whole stack (or hyperstack) and then compute the threshold based on that histogram. As such, all slices are thresholded using the single computed value. If unchecked, the threshold of each slice is computed separately. Default setting is unchecked.

Resampling: This panel contains parameters specifically related to the resampling of the selected image before thresholding.

Resolution: The resolution in pixels (1/scale factor) used by the automatic thresholding methods to resample the selected image before thresholding. Note that a value of 1 will keep the actual resolution of the selected image.

Method: The method used to resample the selected image before thresholding. Three resampling methods are possible: None, Bilinear and Bicubic interpolation (see ImageJ Documentation for more details).

AutoLocal threshold: This panel contains parameters specifically related with local thresholding methods when selected.

Radius: Sets the radius in pixels of the circular window over which the local threshold will be computed (See Fiji Auto Local Threshold for more details). Any number different than 0 will change the default value.

Parameter 1/2: Sets specific values for each method (See Fiji Auto Local Threshold for more details). Any number different than 0 will change the default value.

Image Treatment: If checked, a set of functions will be applied on the specified channel of the active image before thresholding. The functions are defined using the ImageJ macro code (see Intro to Macro Programming for more details). Note that the macro will run on a transient version of the image and will not permanently change the original image. Note that if the resulting image is not already thresholded, the final binary mask will be generated using the specified thresholding method.

Threshold calculator: If checked, a specific set of actions on the selected image will be used to generate the final binary mask. Three actions are possible: Thresholding, Process and Operation. Each action generates a transient binary mask accessible by the subsequent steps using its index. Note that only the last binary mask will be used to detect Particle.

Thresholding : Adds a “thresholding” action and selects the parameters to generate a binary mask from the specified channel of the active image: the channel, the type of background, the method of auto-thresholding and an offset (see Threshold for more details).

Process : Adds a “Process” action and selects the parameters to process the specified binary mask and saves a copy at the specified index. Eight processes are available: Erode, Dilate, Open, Close, Outline, Skeletonize, Fill holes and Median (see ImageJ Binary Process for more details). Note that the Threshold calculator assumes that objects are black and background is white.

Operation :  Adds a “Process” action and selects the parameters to perform arithmetic and logical operations between two specified Binary masks. Four arithmetic and logical operations are available: AND, OR, XOR and Subtract (see ImageJ Image Calculator for more details).

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