Image visualisation

Displays 3D data as 2D montages of all slices.

The aim of this plugin is to characterise the orientation and isotropy properties of a region of interest (ROI) in an image, based on the evaluation of the gradient structure tensor in a local neighborhood. 

TrakEM2 is an ImageJ plugin for morphological data mining, three-dimensional modeling and image stitching, registration, editing and annotation (Fiji comes with TrakEM2). It supports arbitrary-sized datasets. 

Use Icy as an image viewer from Matlab.

JRuby script that will take an image stack and generate from it an image that should appear in 3D when viewed through red and cyan glasses. All that this does is to do two maximum intensity projections from two slightly different angles and merges them together.

Volocity Visualization is designed to provide rapid, interactive, high resolution volume rendering of multi-channel 3D and 4D data sets. This Volocity product puts you in control of the way that you view your 3D data, offering a choice of rendering methods so that you can achieve the best results.  A range of file formats can be imported from  wide field and confocal microscopes, and snapshots and movies can be created quickly and easily to share and publish.

display-shiny

Wavelet-based method to merge a stack of micrographs taken at different focal positions (aligned along the optical axis) into a single, entirely focused composite image.

This plugin provides an extended depth of field algorithm to obtain in focus microscopic images of 3D objects and organisms using different algorithms: Sobel, variance, real and complex wavelets.

View a single channel of a 2D image as a 3D elevation map (X,Y,Intensity).

PSF Generator is a software package that allows one to generate and visualize various 3D models of a microscope PSF. The current version has more than fifteen different models.

3D diffractive models: scalar-based diffraction model Born & Wolf, scalar-based diffraction model with 3 layers Gibson & Lanni, and vectorial-based model Richards & Wolf, and Variable Refractive Index Gibson & Lanni model.

Defocussing a 2D lateral function with 1D axial function: the available lateral functions are: "Gaussian", "Lorentz", "Cardinale-Sine", "Cosine", "Circular-Pupil", "Astigmatism", "Oriented-Gaussian", "Double-Helix".

Optical Transfer Function generated in the Fourier domain: Koehler simulation, defocus simulation.