Open Source MATLAB Image Processing Software

Analysis Nuclei DAB (AND) Tool is a Graphical User Interface (GUI) to analyse microscopy images representing cells with nuclei stained using DAB dyes. The tool requires as input the original RGB images, and the FastRed, FastBlue, DAB channel, easily obtained using the Fiji function: "ImageJ" -> "Image" -> "Colour Deconvolution" -> "FastRed FastBlue DAB" Then, the tool first segment the nuclei using the FastBlue channel and the DAB channel, and then computes statistics by subdividing the sample in three regions according to the FastRed channel: a dark-red ROI, a light-pink ROI and a white ROI. ANDTool is written in MATLAB (The MathWorks, Inc., Massachusetts, USA) and the source code and standalone versions are here available for download. USER MANUAL: see the specific PDF available in the Files section. REQUIREMENTS: MATLAB R2017b and Image Processing Toolbox 10.1 or later versions. MAIN CONTACT: Filippo Piccinini (E-mail: filippo.piccinini85@gmail.com)

This MATLAB-based program enables analysis of AFM images. In particular, it allows the user to measure the volume of all distinguishable features in an image and to isolate and sort those particles. As the name implies, LAVA uses Lloyd's Algorithm, also known as k-means sorting, to identify a small set of volumes representative of the actual distribution of particle in the image. Although developed for determining feature volume, LAVA is also completely compatible with other types of image analysis, such as fluorescence intensity. Work is in progress to provide three-channel functionality, allowing comparison of relative intensity of red, green, and blue channels in multi-color images.

Reconstruction and Visualization from Multiple Sections (ReViMS), an open-source, user-friendly software for automatically estimating volume and several other features of 3D multicellular aggregates (i.e., cancer spheroid, zebrafish, fruit fly). ReViMS requires a z-stack of 2D binary masks, obtained by segmenting a sequence of fluorescent images acquired by scanning the aggregate along the z axis, using a confocal or a light-sheet fluorescent microscope. It provides a number of tools for: (a) segmenting z-stacks of fluorescence images; (b) reconstructing the 3D surface of the aggregates and estimating several features (including the volume). ReViMS is written in MATLAB (The MathWorks, Inc., Massachusetts, USA). It is an open-source tool and the source code is freely available at: http://sourceforge.net/p/revims Requirements: MATLAB R2017b and Image Processing Toolbox 10.1 or later versions.

TracTrac is a Particle Tracking Velocimetry (PTV) software which is extremely fast (more than 10k points tracked per second, 100k under python) and accurate (up to 0.01 pixel resolution), forming thus a good concurrent to the state-of-the art PIV/PTV algorithms. It allows to track anything that moves: birds, ants, grains, water flows... It runs on Python (v2&3) or Matlab (>2012a with Image Processing toolbox). Give it a try ! Get the last sources on GitHub: https://github.com/jorishey1234/tractrac

MatLab App for calculating fitting isotopic exchange profile data. Developed for measuring self-diffusivity and effective surface exchange coefficient of ion conducting materials. Requires MatLab image processing toolbox If you use this tool for you research, please cite my PhD thesis: Cooper, S. J. Quantifying the Transport Properties of Solid Oxide Fuel Cell Electrodes. (Imperial College London, 2015). @phdthesis{SJCooper2015, author = {Cooper, S. J.}, number = {November}, publisher = {Imperial College London}, school = {Imperial College London}, title = {{Quantifying the Transport Properties of Solid Oxide Fuel Cell Electrodes}}, year = {2015} }

A general flow visualization Matlab toolbox for image processing of some common planar/surface visualization techniques from PLIF (Planar laser induce fluorescence) for tracer distribution, BOS (background oriented Schlieren) for density, TSLC (Temperature sensitive liquid crystal) for thermal and PSP (Pressure sensitive paint) pressure distribution measurement. This work is part of author's PhD study, under Dr S. Zhong @ the University of Manchester's supervision, guidance and support. Both GUI and command line interface are provided for newbie and advanced user. Image can be processed into contour image, matlab mat and tecplot data. This toolbox can be conveniently extended for 2D image processing in other disciplines, for example, surface stress measurement, inferred thermograph, PIV. See developer guide for HOWTO. * example project.mat and calib.mat use abs path will not work for you directly. pl. rebuild yours according to my youtube tutorial