Segmentation, or the ability to distinguish an object from its background, can be a difficult issue to deal with. Manual particle counting can be done using the Multi-point Tool. For a complete list of the methods available with Fiji see the Plugins section located in the Documentation section under the Content tab at the top of this page. Automatic particle counting can be done if the image does not have too many individual particles touching. These include Otsu's thresholding, maximum entropy threshold, and mixture modelling thresholding. (2004), "Survey over image thresholding techniques and quantitative performance evaluation.", Journal of Electronic imaging 13(1): 146-168 ( on Google Scholar).įiji has several plugins found in the menu Image › Adjust › Threshold for automatic calculation of an image threshold. Thresholding is done by choosing a pixel intensity value above which the pixel will be rated as belonging to a particle, below this it will be set as background. The third circle from the left is about 20 microns and I want to count all the particles that meet that threshold. 5.1 Automatic Particle counting The biggest issue is one referred to as segmentation which is to distinguish the object from the background. Is there a good algorithm for detecting particles based on size For example, I have the following image, and I want to detect and count particles that are highlighted in the below image: Its basically based on size. An evaluation of over 40 of these can be found in this paper: If automatic particle counting cannot be done, ImageJ can facilitate manual counting with the Point Picker or Cell counter plugin. There are many algorithms you can use to calculate the threshold without introducing user-bias. The image can be converted to a binary image via the menu command Image › Type › 8-bit. The background of the thresholded image can be made light or dark. A user-friendly ImageJ plugin enables the application and training of U-Nets for deep-learning-based image segmentation, detection and classification tasks with minimal labeling requirements. The Color space option allows you to choose between HSB, RGB, Lab, and YUV. The Threshold color option allows you to choose between Red, White, Black, or B&W as the thresholding color. The Thresholding method option allows you to choose a thresholding techniqe other than the default. For color images, setting the threshold is done with the command sequence Image › Adjust › Color Threshold.
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