Automated

The 3D Rotation plug-in allows you to record a 360 degree rotation of the current focused 3D VTK viewer about the vertical screen axis.

The 'angle step' parameter indicates the deviation in degrees between two consecutive snapshots. Increasing the angle will increase rotation speed (up to a point where it might look like jumping more than rotating) and reduce the final movie length.

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.

The purpose of this plugin is to create a text file with a list of files from Gatan’s 3View montage image stacks. This text file can then be used to automatically import all the images into TrakEM2, as they are, stored in the original directories.

This plugin can find the smallest bounding box of an image (or a rectangular part defined by a selection) by cropping as much background as possible. Found in Fiji, under Image> Adjust.

In the version labeled with (guess background color), the plugin tries to determine the background color by looking at the pixels on the border of the image, while Auto Crop uses the currently selected background color which can be changed by double-clicking on the pipette symbol or using the Image > Color > Color Picker....

Instead of cropping right away, you can set the selection to the rectangle that would be cropped to using Edit > Selection > Select Bounding Box.

This plugin perform various 3D filters on 8-bits or 16-bits gray-levels stacks :

• 3D median

• 3D mean

• 3D minimum

• 3D maximum

• 3D maximum local

• 3D tophat (detect bright spots, TH=I-max(min(I)) )

Converts objects you have identified into an image.

This plugin registers (= aligns, matches) a stack of image slices.

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.

Fast Fourier Transform (FFT) for 2D/3D images.

This module classifies objects into a number of different bins according to the value of a measurement (e.g., by size, intensity, shape). It reports how many objects fall into each class as well as the percentage of objects that fall into each class. The module asks you to select the measurement feature to be used to classify your objects and specify the bins to use. It also requires you to have run a measurement or CalculateMath previous to this module in the pipeline so that the measurement values can be used to classify the objects.

An example ImageJ plugin illustrating how to create and display 3D tubes and 3D spheres in the 3D Viewer.

This plugin provides some useful functions to work with complex-valued sequences.

It provides the base operation to deal with complex-valued sequences, such as real-part, imaginary-part, modulus and argument extraction, and conversion between Cartesian and polar representation.