Software Listing of Author : "Jean-yves Tinevez"

CHECKFIELD intend to be a facility to handle varargin in functions. It provides error checks, default, and structuring for the varargin. k = CHECKFIELD(field,listfield) where field is a string checks if field is one of the fields in the cell listfield given in second argument. It returns the index of the found field in the list if successful. K = CHECKFIELD(argin,listfield) where argin is a cell of arguments pair, first checks if field/value come by pair, and then if the fields are in the cell listfield given in second argument. It returns the array of index of the fields in the list if successful. S = CHECKFIELD(field,value,TESTVALID) checks the contents of the specified value to be valid for the field 'field', by applying it to the function handle TESTVALID, which must be a function that returns a boolean. S =...

  • Platform: Matlab, Scripts

ImageJ is an image processing software, very popular in the Life-Science field. If you are a master student, a PhD or a postdoc in Biology, there is a very good chance that ImageJ is installed on your computer. ImageJ is developed mainly by Wayne Rasband, and is written in Java (see http://rsb.info.nih.gov/ij/index.html). It has a clever plugin system that allows users to extend it with new functionalities. Fiji (Fiji is Just ImageJ, http://fiji.sc/) is a distribution of ImageJ, that includes (amongst other things) a lot of plugins, some useful libraries and an updater to keep everything up to date. Amongst other things, it is made to facilitate inter-operability with other softwares. For instance, it offers scripting facilities using popular languages such as Python, Ruby, Clojure, Beanshell, javascript, etc. It also ships with...

  • Platform: Matlab, Scripts

PLOTSTATS(XDATA,YDATA) generate a nice figure for the statistical visualisation of datasets. YDATA is a cell array of vectors, each vector being a group of samples to test. XDATA is a cell array of the same size of YDATA, each element being a single number representing the abscissa of the corresponding sample group in YDATA. XDATA can be omitted. Example: ydata = { [ 1 2 3 4 5 6 7 8 9 ] [ 2 3 4 5 ] 10*rand(10,1) }; xdata = { 1 2 3 }; ydata ydata = [ 1x9 double] [ 1x4 double] [10x1 double] xdata xdata = [1] [2] [3] plotstats(xdata,ydata) With this default syntax, the command generate a 2-panel figure. The first one containing the raw data plot, the second one the box plot. It is possible to extensively customize the generated plot. See inline help for details. -------- EXAMPLES -------- % Basic plot x = {1 2 4};...

  • Platform: Matlab, Scripts

SIMPLETRACKER a simple particle tracking algorithm that can deal with gaps *Tracking* , or particle linking, consist in re-building the trajectories of one or several particles as they move along time. Their position is reported at each frame, but their identity is yet unknown: we do not know what particle in one frame corresponding to a particle in the previous frame. Tracking algorithms aim at providing a solution for this problem. |simpletracker.m| is - as the name says - a simple implementation of a tracking algorithm, that can deal with gaps. A gap happens when one particle that was detected in one frame is not detected in the subsequent one. If not dealt with, this generates a track break, or a gap, in the frame where the particle disappear, and a false new track in the frame where it re-appear. |simpletracker|...

  • Platform: Matlab, Scripts

A per-value class that implements a generic tree data structure. A tree is a hierarchical data structure where every node has exactly one parent (expect the root) and no or several children. Along with this relational structure, each node can store any kind of data. This class implements it using plain MATLAB syntax and arrays. Most useful methods are implemented, using overloading of MATLAB functions for tree objects. For instance you can type: >> find ( (a.^2 .* b) > (c - 5) & d ) with a, b, c and d being tree objects. Very handy, trivial to use. A rather long tutorial is included to walk you through trees, and show how to make the best out of them.

  • Platform: Matlab, Scripts
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