plugin

ADAPT is capable of rapid, automated analysis of migration and membrane protrusions, together with associated
fluorescently labeled proteins, across multiple cells. ADAPT can detect and morphologically profile filopodia.

ADAPT (Automated Detection and Analysis of ProTrusions) is a plug-in developed for the ImageJ/Fiji platform to automatically detect and analyse cell migration and morphodynamics. The program provides whole-cell analysis of multiple cells, while also returning data on individual membrane protrusion events. The plug-in accepts as input one or two image stacks and outputs a variety of data. ADAPT may also be run in batch mode.

The ImageJFX Project aims to create a new user interface for the software ImageJ in order to ease scientific image analysis. While keeping the core components of ImageJ, ImageJFX brings scientists closer to their goal by making the interface clearer for beginners and more practical for advanced users.

SIMcheck is an ImageJ plugin suite for assessing the quality and reliability of Structured Illumination Microscopy (SIM) data. The quality of the raw data, the quality of the reconstruction and the calibration of the microscope can be tested. 

This module is for learning classification models from ground-truth data (supervised learning). It downloads from Cytomine-Core annotation images and coordinate of annotated objects from project(s) and build a annotation classification model which is saved locally.  

It is used by Cytomine DataMining applications: classification_validation, classification_model_builder, classification_prediction, segmentation_model_builder and segmentation_prediction. But it can be run without Cytomine on local data (using dir_ls and dir_ts arguments).

A resident function in ImageJ, located in the menu as [Process > Binary > Voronoi].

Quote from the ImageJ reference page:

Splits the image by lines of points having equal distance to the borders of the two nearest particles. Thus, the Voronoi cell of each particle includes all points that are nearer to this particle than any other particle. When particles are single points, this process is a Voronoi tessellation (also known as Dirichlet tessellation). The output type (Overwrite, 8-bit, 16-bit or 32-bit) of this command can be set in the [Process > Binary > Options...] dialog box. In the output, the value inside the Voronoi cells is zero; the pixel values of the dividing lines between the cells are equal to the distance between the two nearest particles. This is similar to a medial axis transform of the background, but there are no lines in inner holes of particles.

An object detection function in ImageJ. [Analyze > Analyze Particles...]. It could simply be used for counting number of cells, but could also do more complex stuffs. ## Jython Snippet Here is a snippet of how to use Particle Analysis in Jython script.

WaveTracer is a plugin for Metamorph. It represents a functional method for real-time reconstruction with automatic feedback control, without compromising the localization accuracy. It relies on a wavelet segmentation algorithm, together with a mix of CPU/GPU implementation.

This plugin allows : Calculating co-localization between objects in 3D Measuring 3D distances between nearest object, co-localized or not Getting some 3D measurements about each objects The plugin can be used with labelled images, but it also integrates tools for the segmentation of the objects. Programming language: JAVA Processes: Denoise filter Segmentation of the objects Object based co-localization and distance analysis Counting and measurements on objects

Image-processing algorithms developed at the MOSAIC Group for fluorescence microscopy. Tools included:

• 2D/3D single-particle tracking tool which can be used to track bright spots in 2D/3D movies over time.
• Optimal filament segmentation of 2D images. 
• Curvature filters for image filtering, denoising, and restoration. 
• Image naturalization for image enhancement based on gradient statistics of natural-scence images. 
• Tool for automatically send and distribute jobs on clusters and get back the results.
• Multi-region image segmentation of 2D and 3D images without needing to know the number of regions beforehand. 
• Squassh for globally optimal segmentation of piecewise constant regions in 2D and 3D images and for object-based co-localization analysis. 
• Tool for inferring spatial interactions between patterns of objects in images or between coordinates read from a file.
• Tool for robust, histogram-based background subtraction well suited to correct for inhomogeneous illumination artifacts.
• A tool to estimate the Point-Spread Function of the microscopy out of 2D fluorescence images.
• A tool to measure the 3D Point-Spread Function of a confocal microscope from an image stack.
• Addition of synthetic Poisson-distributed noise to an image in order to simulate shot noise of various signal-to-noise ratios. 
• Convolution of an image with a Bessel function in order to simulate imaging with a microscope. 
• A utility to detect bright spots in images and estimate their center. 
• A utility to create manual segmentations to be used as ground truth to test and benchmark automatic segmentation algorithms.
• A tool for replacing one color in an image with another color.