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 All measures given by DiameterJ are in pixels by defaultĭiameterJ has been validated with over 130 digital images created in silico and with scanning electron microscope images of reference wires with known diameters.įibers that are smaller than 10px or greater than 10% of the smallest dimension of the image produce 10% or greater errorįor now DiameterJ only analyzes.the black and white images do not produce an accurate representation of the original image) then DiameterJ will still work with any binary image that has been segmented through some other means. If the user is not happy with the results of the segmentation algorithms (i.e.However, these algorithms may not work for all SEM images. Sixteen default segmentation algorithms have been included with DiameterJ in the “Segment SRM” and “Segment Mixed” plugins.Image Segmentation into a binary image (black and white pixels only).( Bottom) A few of the graphs capable of being produced from data given by DiameterJĭiameterJ 1 is a two step process of image analysis: Overview of DiameterJ analysis flow - ( Top) SEM image → segmented image → stylized Euclidean distance transform. DiameterJ also bundles OrientationJ 2 for a complete analysis of fiber orientation within an image as well as the “Analyze Particles” function built into ImageJ/Fiji to analyze pore space within scaffolds and produce summary statistics for pores. Included with this histogram are summary statistics such as mean fiber diameter and most occurring fiber diameter (mode). DiameterJ is able to analyze an image and find the diameter of nanofibers or microfibers at every pixel along a fibers axis and produces a histogram of these diameters. DiameterJ is a validated nanofiber diameter characterization tool. Nanofiber diameter measurement, nanofiber diameter analysis, nanofiber diameter characterization, nanofiber diameter software, nanofiber diameter plugin, nanofiber diameter program, ImageJ nanofiber diameter, Fiji nanofiber diameter, automated nanofiber diameter, free, open source, radiusĭiameterJ 1 is a free, open source plugin created for ImageJ, ImageJ2, and Fiji developed at the National Institute of Standards and Technology. ImageJ 1.48a to 2.XXX DiameterJ v1.018 Fiji any version DiameterJ v1.018
ImageJ 1.48 or newer (including ImageJ2) and Fiji
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