![]() ![]() If you find this plugin useful for your work, please refer to 3D ImageJ Suite and cite this paper : A generic classification-based method for segmentation of nuclei in 3D images of early embryos. For instance touching cells may result in close nuclei, at low contrast and low threshold the two nuclei may seem like touching and form only one object, however at high threshold two separate objects are being seen.ĭividing objects with thresholds, top left raw image with high brightness, top right raw image with adjusted contrast to distinguish the dividing nuclei, bottom left first channel of Iterative thresholding showing brighter and smaller objects, bottom right second channel of Iterative thresholding showing merged nuclei for lower threshold. Testing all thresholds may lead to objects being divided into smaller objects for high thresholds. Iterative thresholding using different criteria, bottom left elongation, top right volume and bottom right MSER. The contrast refers to the range of thresholds where the object exists, noise or very faint objects may have very low contrast as opposed to very contrasted object. ![]() The image can be filtered before thresholding with a 3D median filter with radii proportional to the minimal volume. In order not to test low thresholds you can specify to start with the mean value of the image as the lowest threshold or specify manually the lowest threshold to start with. Note than the more threshold tested the more memory used. For 16-bits images try Step with values between 5 and 100 depending on the dynamic of your data.
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