Plot Van Hove Correlation plot using @msdanalyzer?
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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
on 20 Jun 2021
Hello,
Did you figure out how to plot the van hove correlation function from these tracks?
Kind regards,
hiteshika
Answers (1)
Edin
on 13 Jun 2023
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
Afterwards, you can put the "convertedTracks" variable into this program on the File Exchange: https://www.mathworks.com/matlabcentral/fileexchange/118310-track_analysis?s_tid=FX_rc1_behav
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