Plot Van Hove Correlation plot using @msdanalyzer?

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Minhaz ur Rahman
Minhaz ur Rahman 2020-3-25
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)?
  2 个评论
hiteshika gosain
hiteshika gosain 2021-6-20
Hello,
Did you figure out how to plot the van hove correlation function from these tracks?
Kind regards,
hiteshika

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回答（1 个）

Edin
Edin 2023-6-13
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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