#Imagej threshold selection gui how to#

The user also controls the size of the smallest quadtree region (aka leaflet). Once the regional thresholds are computed, they are interpolated (bilinear interpolation) across the entire image yielding a threshold map. In our experience, regional threshold failures are rare. It is possible that thresholds fail all the way up the quadtree heirarchy, in which case a same threshold is applied to all regions which is identical to applying a global threshold. In such cases, the regional threshold is replaced by the threshold of its parent quadtree (if the parent’s threshold doesn’t fail). Occasionally, the regional threshold fails if the sum of the weights (the denominator) falls to the level of background containing only noise. Within each of the smallest subregions, a regional threshold,, is computed as the gradient weighted sum of the pixels, P. The input image is then subdivided into a quadtree architecture (for more info see Wikipedia:Quadtree). Estimate the noise by selecting a “background” portion of the image and using ImageJ to determine the standard deviation of gray values. The threshold is defined by an estimate of the noise ( ,the standard deviation of the expected background is a good starting point) and a scaling factor (, 3 is a good starting point). Pixels with gradients that fall below a user specified threshold,, are rejected. In the plugin the gradient is left simply as the sum of the squares of the kernel operations. However, Wilkinson shows that eliminating the square root yields suitable results with out the added cost of a final scan across the image to compute the root. The kernel operators are detailed in many sources including here. Traditionally the Sobel gradient is computed using In this implementation the input gradient of the input image is computed using the Sobel kernels. Chapter 6 in: Wilkinson MHF, Schut F (eds.) Digital Image Analysis of Microbes: Imaging, Morphometry, Fluorometry and Motility Techniques and Applications, Vol. Wilkinson MHF (1998) Segmentation techniques in image analysis of microbes.The plugin is based upon the description in The RATS algorithm is applied across regions of the image making it suitable for thresholding noisy images with variable background. Robust Automatic Threshold Selection (RATS) computes a threshold map for a 2d image based upon the value of pixels and their gradients.

#Imagej threshold selection gui how to#

If you’d like to help, check out the how to help guide! The content of this page has not been vetted since shifting away from MediaWiki.