Fluorescence microscopy

An ImageJ plugin for evaluate intra-nuclear 3D cross-distances between fluorescent spots in multi-channel images 

Identify objects (as nuclei) within an image without needing the assistance of another cellular feature (as cell). 

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.

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MeasureObjectIntensityDistribution measures the spatial distribution of intensities within each object.

Old Name: MeasureObjectRadialDistribution

Colocalizer block.

The Sholl technique is used to describe neuronal arbors. This plugin can perform Sholl directly on 2D and 3D grayscale images of isolated neurons. Its internal algorithm to collect data is based upon how Sholl analysis is done by hand — it creates a series of concentric shells (circles or spheres) around the focus of a neuronal arbor, and counts how many times connected voxels defining the arbor intersect the sampling shells. The major advantages of this plugin over other implementations are:

• When analyzing images directly, it does not require previous tracing of the arbor (although it can also analyze traced arbors)
• It combines curve fitting with several methods to automatically retrieve quantitative descriptors from sampled data, which allows direct statistical comparisons between arbors
• It allows continuous and repeated sampling around user-defined foci
• It allows batch processing

This plugin permit to measure the signal spread of a molecule with respect to the cell area.

An ImageJ plugin for manually tracking objects by mouse clicking. 

This plugin is bundled with Fiji. 

This plugins allows debleaching of time sequences of fluorescence images.

TrackMate provides the tools to perform single particle tracking (SPT). SPT is an image analysis challenge where the goal is to segment and follow over time some labeled, spot-like structures. Each spot is segmented in multiple frames and its trajectory is reconstructed by assigning it an identity over these frames, in the shape of a track. These tracks can then be either visualized or yield further analysis results such as velocity, total displacement, diffusion characteristics, division events, etc...