![]() ![]() Also choose the approximate size of the point spread function (PSF) in your images, as well as the number of iterations to run the Costes statistical significance test (We suggest a large number… the larger the number, the longer the analysis will take.Turn the options on/off by clicking the selection button at the left of the Algorithm description.Numerical results and image names are dumped into the ImageJ Log window as comma separated values, so you can copy paste, or save the log window contents, to then import them into whatever statistical package or spreadsheet in which you wish to analyze the results.Choose which “Algorithms” are run and which statistics you wish to calculate, and if you want to save the “standardized” PDF result file, when the OK button is pressed.remember: for the mask image - it must have the same xyz dimensions (number of pixels and slices) as the other 2 images.In the third drop down list selection, select the image/channel you want to use that has the correct ROI or mask image.Select the images according to which you want to be channel 1 and which to be channel 2.In the plugin’s graphical user interface (GUI) choose the 2 images you want to analyze in the first 2 drop down lists.or use the search bar: press L then start typing coloc, then choose the plugin with the arrow keys and press ↵ Enter, or Double Click it to launch the plugin.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)
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