5/17/2023 0 Comments Imagej thresholdingPlease note that the plugins described here use additional classes also residing in the Morphology collection, so those need to be installed, too. The Java code is included in the Morphology collection. The regional threshold plugin is called Threshold_Regional_Gradient.įurther details of the algorithms, performance and examples are included in our paper accessible through Open Access. Note that this is a computationally intensive procedure, so it is relatively slower than most other thresholding methods that process, for example, one dimensional histograms. The boundaries representing the highest gradients are then extracted by means of the regional maxima of the projection.įurthermore, when combining filtering of the candidate regions based on morphological descriptors such as circularity and region size, the approach allows an efficient and clean extraction of the regions which exhibit the highest gradients. Then, the binary boundaries are labelled with that value and the ensemble of all boundaries is projected, retaining the maximum values (a maxima Z projection). The boundaries of the binary regions thus generated are used to query the value of the average gradient at those positions in the original image. The procedure involves first a threshold decomposition step (where regions are extracted at all possible threshold ranges (e.g. candidate binary regions that might represent the intended object in the image) independently, therefore becoming an adaptive local thresholding procedure which operates on regions, rather than on pixels of local image subsets as is the case in the vast majority of local thresholding methods in the literature. The second method is a more interesting and complex variation of the same principle, but operates on the discrete connected components of the thresholded phase (i.e. The plugin is called Threshold_Global_Gradient and it has the option of using two possible measures of the phase gradient (the mean and the total gradient). The procedure consists of searching the greyscale space for a threshold value that generates a phase whose boundary coincides with the largest gradients in the original image. The first one is a simple global thresholding procedure suitable for single or multiple global thresholds (i.e. The advantage of the computerised versions presented here is that the methods do not suffer from the uncertainty of “when to stop adjusting” the threshold. Users most often find the “right” threshold value by repeatedly over- and under-thresholding the image until the thresholded phase more or less coincides with the sought objects in the image. The procedures implemented are based on a reinterpretation of the strategy observed in human operators when adjusting thresholds manually and interactively by means of ‘slider’ controls. We would be grateful if you cite the paper in any publications where you use these methods (and let us know about it). Automatic thresholding from the gradients of region boundaries. The two thresholding plugins discussed in this page are part of the Morphology collection.įor a detailed description of the methods, please see: Landini G, Randell DA, Fouad S, Galton A.
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