Plot Van Hove Correlation plot using @msdanalyzer?

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)?

[hiteshika gosain]

Hello,

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

Kind regards,

hiteshika

[MINHAZ RAHMAN]

Not yet...could you?

Answer 1

[Edin]

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