Erosion (through ImageJs erode command, and dilation (through ImageJs dilate command), and a final erosion (through ImageJs erode command), operations served to refine the image, highlighting fiber edges and eliminating isolated pixel areas. ![]() Briefly, successive rounds of noise removal (via ImageJ’s despeckle command) were performed until no change in the image was found. Additionally, we use more conventional segmentation algorithms developed by Otsu 4, Huang 5, Kittler (min error) 6, Doyle (percentile) 7, or Zack (triangle) 8Īfter segmentation all images had remaining noise and morphological features that were smoothed according to the protocols outlined by D’Amore 9 and by Gonzalez 10. Specifically, we have found that for SEM images of nanofibers the Statistical Region Merging algorithm 3 developed by Johannes Schindelin does a great job of blending fibers across their diameter and by depth to create great representations of the fibers when they are segmented. Both the Segment SRM and Segment Mixed plugins are automated inclusions of others segmentation algorithm work. SEM micrographs were first segmented using a variety of thresholding techniques available in ImageJ/Fiji. For a block diagram and overview of how the DiameterJ algorithm analyzes fiber diameter and other scaffold properties see below. The overall goal of the DiameterJ 1 algorithm was to be able to analyze an 8-bit SEM image of any resolution using a desktop computer in less than 60 seconds. 1.018 for ImageJįor Fiji latest release: DiameterJ v. DiameterJ: A validated open source nanofiber diameter measurement tool. Hotaling NA, Bharti K, Kriel H, Simon Jr. If you would like to cite DiameterJ in your work, use the below: Citation/Reference Information gif filesįibers must be less than 512px in diameter to be analyzed
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