#Imagej threshold selection code#
The code in ImageJ that implements this function is the getAutoThreshold() method in the ImageProcessor class. System, Man and // Cybernetics, SMC-8 (1978). thresholding using an iterative selection method, IEEE Trans. Note that there are many more methods for setting an automatic threshold (such as Otsu's method, entropy method, triangle method, k-means clustering, etc). Contribute to fiji/AutoThreshold development by creating an account on GitHub. Threshold = (average background + average objects)/2 The averages of those two values are computed, the threshold is incremented and the process is repeated until the threshold is larger than the composite average. Discrete early endosomes that fused together during thresholding are separated using the ImageJ paintbrush tool (brush width set to 13 pixels, as necessary for precision). The online Image Processing Fundamentals tutorial discusses the isodata algorithm among several others.īriefly, the procedure divides the image into objects and background by taking an initial threshold, then the averages of the pixels at or below the threshold and pixels above are computed. In Step 3 of the ImageJ protocol, the ROI within the 3D reconstruction is designated by tracing the outline of the BFCN using ImageJ’s freehand selection tool.The automatic thresholding function used by Image>Adjust>Threshold and Process>Binary>Threshold is an iterative procedure based on the isodata algorithm Area Fraction- The percentage of pixels in the image or selection that have been highlighted in red using Image>Adjust>Threshold. What is the algorithm used by ImageJ to find the ideal threshold value?