Rank: 272 based on 389 downloads (last 30 days) and 10 files submitted
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Jean-Yves Tinevez

E-mail
Company/University
Institut Pasteur
Lat/Long
48.84045, 2.311

Personal Profile:
Professional Interests:
signal processing, image processing, biology, imaging

 

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Files Posted by Jean-Yves View all
Updated   File Tags Downloads
(last 30 days)
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10 Jul 2014 Screenshot Tree data structure as a MATLAB class A per-value class that implements a generic tree data structure. Author: Jean-Yves Tinevez matlab, data structure, tree, graph, tutorial, oop 87 41
  • 4.85714
4.9 | 17 ratings
08 Jul 2014 Screenshot Mean square displacement analysis of particles trajectories A MATLAB class for the mean square displacement analysis of particle trajectories, with a tutorial. Author: Jean-Yves Tinevez measurement, simulation, statistics, physics, image processing 69 22
  • 5.0
5.0 | 8 ratings
21 Feb 2013 Screenshot Circle pixel coordinates using mid-point algorithm Return the optimal pixel coordinates of a circle, given its center and radius. Author: Jean-Yves Tinevez image processing, drawing, center, circle 39 2
  • 4.5
4.5 | 2 ratings
25 Jan 2013 Screenshot Rolling statistics Convenience utility made to compute descriptive statistics without storing data. Author: Jean-Yves Tinevez signal processing, image processing, data exploration, statistics, demo, measurement 10 0
20 Aug 2012 Screenshot Simple Tracker Simple multiple particle tracker with gap closing. Author: Jean-Yves Tinevez tracking, image processing, particle linking 56 9
  • 4.75
4.8 | 9 ratings
Comments and Ratings by Jean-Yves View all
Updated File Comments Rating
10 Oct 2014 Mean square displacement analysis of particles trajectories A MATLAB class for the mean square displacement analysis of particle trajectories, with a tutorial. Author: Jean-Yves Tinevez

Hi @Liam, and thanks for the feedback.
What you mention here resembles a known bug. If the frame interval of the movie you want to analyze is defined over too many digits (something like 0.18374531289123648392716 seconds), the class gets confused when binning intervals together, which ultimately triggers the error you got.
Could you please check what is the frame interval in your case? Cropping it to a few digits should solve the problem.
Best
jy

27 Sep 2014 Tree data structure as a MATLAB class A per-value class that implements a generic tree data structure. Author: Jean-Yves Tinevez

Hi @Muhammad.
In theory nothing prevents you from concatenating all the methods file in the class main file, inside a 'methods' block. Except that it would make the code completely unreadable and unmaintainable. I did this mistake once for another contribution (the msdanalyzer) and won't do it again.
Best
jy

15 Sep 2014 Mean square displacement analysis of particles trajectories A MATLAB class for the mean square displacement analysis of particle trajectories, with a tutorial. Author: Jean-Yves Tinevez

Hi @LM,
I am a great admirer of the u-track software, but I did not create something that can arrange its results into the analyzer, sorry.
Thanks for feedback.

07 Aug 2014 Mean square displacement analysis of particles trajectories A MATLAB class for the mean square displacement analysis of particle trajectories, with a tutorial. Author: Jean-Yves Tinevez

@Vid. Indeed the problem is caused by the frame interval having too many digits. This causes rounding errors while subtracting time position between frames, and some frame intervals are not pooled together.
This a severe flaw, originating from my design choice. Storing the frame intervals in physical units was a bad idea that leads to these errors and the only solution is to rewrite the analyzer and store the frame intervals as integer.
In the meantime, your fix works of course.

06 Aug 2014 Mean square displacement analysis of particles trajectories A MATLAB class for the mean square displacement analysis of particle trajectories, with a tutorial. Author: Jean-Yves Tinevez

@Florent @Johannes. This clearly points to a MATLAB path problem. Remember that msdanalyzer is a class. What does
>> which msdanalyzer
returns?

Comments and Ratings on Jean-Yves' Files View all
Updated File Comment by Comments Rating
10 Oct 2014 Mean square displacement analysis of particles trajectories A MATLAB class for the mean square displacement analysis of particle trajectories, with a tutorial. Author: Jean-Yves Tinevez Tinevez, Jean-Yves

Hi @Liam, and thanks for the feedback.
What you mention here resembles a known bug. If the frame interval of the movie you want to analyze is defined over too many digits (something like 0.18374531289123648392716 seconds), the class gets confused when binning intervals together, which ultimately triggers the error you got.
Could you please check what is the frame interval in your case? Cropping it to a few digits should solve the problem.
Best
jy

08 Oct 2014 Mean square displacement analysis of particles trajectories A MATLAB class for the mean square displacement analysis of particle trajectories, with a tutorial. Author: Jean-Yves Tinevez Liam

Hi Jean-Yves,

Great piece of software! Very useful. However I used it for Imaris tracks analysis and got the following error:

Computing velocity autocorrelation of 152 tracks... [...] 17/152Error using +
Matrix dimensions must agree.

Error in msdanalyser/computeVCorr (line 1266)
sum_vcorr(index_in_all_delays) = sum_vcorr(index_in_all_delays) + lvcorr;

Error in XTMeanSquareDisplacementGrapher (line 137)
msd = msd.computeVCorr;

Do you have a solution for this? (I'm afraid to say I have no knowledge of MatLab language...).

Many thanks!

27 Sep 2014 Tree data structure as a MATLAB class A per-value class that implements a generic tree data structure. Author: Jean-Yves Tinevez Zaman, Muhammad Aneeq uz

Yes I was able to concatenate all the functions I needed in one file and run it (for some reason the 'eq' function doesn't seem to work). But there seems to be another problem, matlab coder won't work with cell arrays so I guess I am out of luck. But thanks any way.

27 Sep 2014 Tree data structure as a MATLAB class A per-value class that implements a generic tree data structure. Author: Jean-Yves Tinevez Tinevez, Jean-Yves

Hi @Muhammad.
In theory nothing prevents you from concatenating all the methods file in the class main file, inside a 'methods' block. Except that it would make the code completely unreadable and unmaintainable. I did this mistake once for another contribution (the msdanalyzer) and won't do it again.
Best
jy

27 Sep 2014 Tree data structure as a MATLAB class A per-value class that implements a generic tree data structure. Author: Jean-Yves Tinevez Zaman, Muhammad Aneeq uz

Hi Jean-Yves, I am trying to compile my project using matlab coder and it is returning error "Cannot load '.../tree/@tree/tree.m' because code generation does not support classes and enumerations in @-directories." So the problem seems to be the @-directory which is needed for a multi-file class definition. Would you have any idea how to convert it into a single file class def?

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