One can specify the “block size,” “histogram bins,” and “max slope” parameters (the details of which are outlined on ), but I have found that the default parameters do a fine job. In the text field, paste the CLAHE script. In FIJI, go to “Plugins” > “New” > “Macro”.Copy the CLAHE script from the “ Tips” section on the website.Wait until FIJI reads in the entire image stack. Drag and drop the folder that contains a stack of CT images into FIJI (download here: ).It is particularly helpful when applied to sub-optimally stained specimens.ĬLAHE is implemented in FIJI ( ImageJ) and the script is available freely and openly. This results in digital contrast enhancement that is not dominated by overly deep blacks or excessively bright whites.įor diceCT, CLAHE is very useful for improving edge recognition for digitally segmenting regions of interest (ROI) based on your CT data. In contrast to standard histogram equalization that applies single formula for enhancing contrast across the entire image, CLAHE applies multiple equalizations within partitions of an image, resulting in more localized and subtle contrast enhancements. Head over to the Journal of Experimental Zoology to download the pub!īy Aki Watanabe ( limited adaptive histogram equalization ( CLAHE) is a procedure for enhancing local contrast in an image or stack of images. We also found a clear positive relationship between glycogen concentration and grayscale values measured within muscle, epithelia, nervous tissues, and glands regardless of the staining solution used.” Mathematical simulations suggest that remarkably different results from I 2 E and I 2 KI-formalin staining are due to different partition coefficients and retardation factors of tissues, fixation effects, and distinct iodine diffusion and sorption patterns. By contrast, we found the I 2 E (iodine-ethanol) treatment can increase the X-ray opacity of not only soft tissues (e.g., muscles), but also the bone. “ I 2 KI-formalin (iodine-potassium iodine-formalin) treatment can obscure the natural X-ray contrast of the bone due to neighboring soft-tissues during staining of avian cephalic material. Black arrows highlight the staining effect on the spinal cord white arrows highlight the differential penetration of iodine in the two approaches (inset 3-D renderings for each specimen show the section positions). Sagittal sections of the two tinamou heads processed using I 2KI-formaldehyde (A) and I 2E (B), respectively.
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