Plot Van Hove Correlation plot using @msdanalyzer?

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Minhaz ur Rahman 2020-3-25

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https://ww2.mathworks.cn/matlabcentral/answers/512954-plot-van-hove-correlation-plot-using-msdanalyzer

回答： Edin 2023-6-13

I am using msdanalyzer (Tinevej et. al. 2013) for Single Particle Tracking Microrheology. Can anyone assist me to how can I plot Van Hove Correlation plot after loading the x,y positions from xml files (which were created using TrackMate via imageJ Fiji plugin)?

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hiteshika gosain 2021-6-20

Hello,

Did you figure out how to plot the van hove correlation function from these tracks?

Kind regards,

hiteshika

MINHAZ RAHMAN 2021-6-22

Not yet...could you?

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Answer 1

Edin 2023-6-13

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https://ww2.mathworks.cn/matlabcentral/answers/512954-plot-van-hove-correlation-plot-using-msdanalyzer#answer_1254909

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Hey there,

I don't know if I'm too late for this, but I just made a small script that should convert msdanalyzer tracks into a variable another MATLAB program can understand, which supports finding the van Hove correlation.

% Convert msdanalyzer tracks to a format Track Analysis understands. Written by Edin O. on 13.6.23 under GPLv3 license.
%% Declare variables
ma = importdata(""); % Path to msdanalyzer variable
SAVE_FILE = false;
%% Calc variables
lTracks = cellfun('size', ma{1}.tracks, 1);
offset  = cumsum(lTracks);
%% Move data
% Init
tr = nan(sum(lTracks), 4);
R = ma{1}.tracks{1}(:,2:end);
frames = 1:lTracks(1);
tr(1:offset(1),:) = [R, frames', ones(lTracks(1), 1)];
% Loop
for i = 2:length(lTracks)
    R = ma{1}.tracks{i}(:,2:end);
    frames = 1:lTracks(i);
    colStart = offset(i-1) + 1;
    tr(colStart:offset(i), :) = [R, frames', repmat(i, lTracks(i), 1)];
end
%% Save
if SAVE_FILE
    save("convertedTracks.mat", "tr", "-v7.3")
end