If the manual file selection mode was choose a file selection dialog will apear:.If this option is not chosen, each output file will be saved in the same directory as the corresponding raw input file. Output to new Folder: Allows to select a folder where all output data is saved.Method for low and high threshold: Select one of ImageJ's core thresholding algorithms to calculate the low and high threshold or choose Custom Value to define a fixed value.
Alpha: The parameters defines the sensitivity of the edge detection.This values might vary with the quality (less noise might allow for less blur and, thus a lower value for sigma). In the test data a sigma of 1 and 0.5 pixels yielded good results for images with 0.1 and 0.2 µm/pixel, respectively. Sigma for Gaussian blur: Defines the amount of blur added to the image as the sigma ("radius") of the Gaussian distribution in pixels.If multi channel stack or raw microscopy file is chosen another dialog the thresholding channel and the set of addtionally saved channels need to be defined in a subsequent dialog. Select image input image format: Choose between single channel stack, multi channel stack, or a raw microscopy file.The pre-selected option ( manual file selection) lets the user select files in a subsequent dialog ( Multi-File-Manager).
txt containing the full paths to the images in separate lines ( use list). File selection mode: Allows to use the active (=last used) image in ImageJ ( active image in FIJI), all images open images ( all images open in FIJI), or to load a previously defined set of files from.In the user dialog the following options are available:.Open ImageJ and select Plugin> SR> Canny 3D Thresholder.The plugin can handle multi-channel (up to 4 channels) timelapse image stacks ("4D") provided either as TIFF stack or as a common Bioformat (e.g. jar files to the ' plugins' directory in the ImageJ folder (' Fiji.app').