THOT

Description

Classification of trajectoire: need tracking results as input and will then classify the trajectories as  brownian motion, confined brownian or directed.

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thot

Adipocyte quantification MATLAB

Description

Analysis of adipocyte number and size. The original code and example images supposed to be discovered at http://webspace.buckingham.ac.uk/klanglands/ but currently the webpage is missing the code and sample images.

has topic
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AVEMAP

Description

Measures wound-healing assay videos, 

 For each video, the velocity and the order parameter are analyzed in time and space to extract quantitative parameters characterizing the cell motility phenotype. The different conditions (videos) can then be classified according to these parameters.

AveMAP

Neural Circuit Tracer

Description

Neural Circuit Tracer (NCTracer) is open source software for automated and manual tracing of neurites from light microscopy stacks of images. NCTracer has more than one workflow available for neuron tracing. 


"The Neural Circuit Tracer is open source software built using Java (Sun Microsystems) and Matlab (MathWorks, Inc., Natick MA). It is based on the core of ImageJ (http://rsbweb.nih.gov/ij) and the graphic user interface has been developed by using Java Swings. The software combines anumber of functionalities of ImageJ with several newly developed functions for automated and manual tracing of neurites. The Neural Circuit Tracer is designed in a way
that will allow the users to add any plug-ins developed for ImageJ. More importantly, functions written in MatLab and converted into Java with Matlab JA toolbox can also be added to the Neural Circuit Tracer." 

Example of output from Neural Circuit Tracer

Rivulet

Description

"we propose a novel automatic 3D neuron reconstruction algorithm, named Rivulet, which is based on the multi-stencils fast-marching and iterative back-tracking. The proposed Rivulet algorithm is capable of tracing discontinuous areas without being interrupted by densely distributed noises." 

This plugin can be used with default parameters or with user-defined parameters.

Example image obtained from Rivulet Wiki website (https://github.com/RivuletStudio/Rivulet-Neuron-Tracing-Toolbox/wiki

Traceplot_Rivulet

Spine classification based on kernel density estimation

Description

We propose to use a kernel density estimation (KDE) based approach for classification. This non-parametric approach intrinsically provides the likelihood of membership for each class in a principled manner. The implementation was used in Ghani2016. Any papers using this code should cite Ghani2016 accordingly. The software has been tested under Matlab R2013b.

 

Sample Data: Annotated two-photon images of dendritic spines

FOCAL

Description

FOCAL (Fast Optimized Cluster Algorithm for Localizations) is a rapid density based algorithm for detecting clusters in localization microscopy datasets.

need a thumbnail

Clus-Doc

Description

Clus-Doc is a software that quantifies both the spatial distribution of a protein as well as its colocalization status. It may be used to quantify signaling activity and protein colocalization at the level of individual proteins.

need a thumbnail

MATLAB Image Segmentation Tutorial

Description

Quote

Perfect for the beginner, this demo illustrates simple object detection (segmentation, feature extraction), measurement, and filtering. Requires the Image Processing Toolbox (IPT) because it demonstrates some functions supplied by that toolbox, plus it uses the "coins" demo image supplied with that toolbox. If you have the IPT (you can check by typing ver on the command line), you should be able to run this demo code simply by copying and pasting this code into a new editor window, and then clicking the green "run" triangle on the toolbar. First finds all the objects, then filters results to pick out objects of certain sizes. The basic concepts of thresholding, labeling, and regionprops are demonstrated with a simple example.

It's a good tutorial for those users new to MATLAB's image processing capabilities to learn on, before they go on to more sophisticated algorithms.

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Cell segmentation in phase contrast images

Description

This Matlab code demonstrates an edge-based active contour model as an application of the Distance Regularized Level Set Evolution (DRLSE) formulation.

initialisation