Image thresholding

VTK is an open-source software system for image processing, 3D graphics, volume rendering and visualization. VTK includes many advanced algorithms (e.g., surface reconstruction, implicit modeling, decimation) and rendering techniques (e.g., hardware-accelerated volume rendering, LOD control).

VTK is used by academicians for teaching and research; by government research institutions such as Los Alamos National Lab in the US or CINECA in Italy; and by many commercial firms who use VTK to build or extend products.

The origin of VTK is with the textbook "The Visualization Toolkit, an Object-Oriented Approach to 3D Graphics" originally published by Prentice Hall and now published by Kitware, Inc. (Third Edition ISBN 1-930934-07-6). VTK has grown (since its initial release in 1994) to a world-wide user base in the commercial, academic, and research communities.

MiNA is a simplified workflow for analyzing mitochondrial morphology using fluorescence images or 3D stacks in Fiji. The workflow makes use of ImageJ Ops, 3D Viewer, Skeletonize (2D/3D), Analyze Skeleton, and Ridge Detection. In short, the tool estimates mitochondrial footprint (or volume) from a binarized copy of the image as well as the lengths of mitochondrial structures using a topological skeleton. The values are reported in a table and overlays (or a 3D rendering) are generated to assess the accuracy of the analysis.

 This ImageJ function automatically or interactively sets lower and upper threshold values, segmenting grayscale images into features of interest and background.

QuantiFish is a quantification program intended for measuring fluorescence in images of zebrafish, although use with images of other specimens is possible. This package is geared towards analysis of fluorescent infection models. The software is designed to automate processing of images of single fish, and outputs results as a .csv file. Alongside measures of total fluorescence above a threshold, this package also introduces several measures for dissemination and distribution of fluorescence throughout the specimen.