ImageJ/Fiji - Segmentation Part 3: Thresholding

Video Highlights and Helpful Links The sample image, “C3-jw-30min 5_c5.tif”, used in this video can be found here (http://workshops.imagej.net/). Thresholding (https://imagej.net/imaging/thresholding) involves choosing a cut-off value to delineate objects from non-objects/background. Auto-Thresholding (https://imagej.net/plugins/auto-thres...) is the recommended technique as it is more objective and reproducible. What happens in the case where you want to measure intensity values on the same channel where you set your threshold? You can potentially bias your results, read more on such pitfalls here on the image.sc forum ( https://forum.image.sc/t/fluorescence.... **Note: The names ‘ImageJ’ and ‘Fiji’ are used interchangeably… we recommend new users download/install/use the Fiji distribution (https://imagej.net/software/fiji/index) of ImageJ, as Fiji Is Just ImageJ!