Launch the Coloc 2 plugin from the menu item: Analyze › Colocalization Analysis › Coloc 2.you can use a z stack as a 3D mask… it’s up to you how you make that mask image, manually or by some automated method.Where it is black (zero pixel value), the pixels will be ignored: not included in the analysis. where the mask image is white (255 pixel value for an 8 bit greyscale image) colocalization will be analyzed for those pixels only.You can have a third “binary mask” image, with the same x,y,z dimensions as the 2 images to be analyzed:.If the image is a z stack, then the ROI applies in all “slices” of the stack.Select a region of interest with one of the ImageJ selection tools, in one of the images.You probably want to analyze only some region of interest (ROI), there are 2 ways to do that:.For now, please split the time series into a numbered set of images and analyse those one by one. But time series will fail until that is fixed. If the image has more than 2 channels, identify the two you want to analyze with each other, then split the channels into separate images (Image- Color - Split Channels) Don’t treat this tool as a black box - try to understand what the strengths and limitations are and what the results could mean.
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