Converted units [dx,dt] from pixels/frames to um./sec

build_xyl_trackmat.m → build_xyl_trackdat.m

@@ -1,7 +1,9 @@
-function [ trackmat_xyl ] =  build_xyl_trackmat ( tracks_input, Nframes )
+function [ trackdat_xyl ] =  build_xyl_trackdat ( tracks_input, px_spacing, Nframes )
 
 Num_comp_tracks = length( tracks_input);
 
+% Loop through each independent track (of length T frames) and figure
+% out how many sub-tracks need to be considered for each case:
 for ti = 1:Num_comp_tracks
 
     Nsubtracks(ti)  =  size( tracks_input(ti).tracksCoordAmpCG, 1);
@@ -12,8 +14,6 @@
     comptrack_death_lag = Nframes - max( tracks_input(ti).seqOfEvents(:,1) );
     % the number of frames that should be appended to the end of this comptrack to make it to the end of the movie.
 
-    % Loop through each independent track (of length T frames) and figure
-    % out how many sub-tracks need to be considered for each case:
     for sti = 1:Nsubtracks( ti )
        % Within each sub-track, extract the position and change values
        % segment in which the particle could not be located on either side
@@ -22,26 +22,26 @@
        % get birth and death time points for each subtrack _within_ the composite window
        obituary = tracks_input(ti).seqOfEvents( tracks_input(ti).seqOfEvents(:,3)==sti, 1 );
 
-       xdat_compwindow = tracks_input(ti).tracksCoordAmpCG(sti,1:8:end);
-       ydat_compwindow = tracks_input(ti).tracksCoordAmpCG(sti,2:8:end);
+       xdat_compwindow = px_spacing * tracks_input(ti).tracksCoordAmpCG(sti,1:8:end);
+       ydat_compwindow = px_spacing * tracks_input(ti).tracksCoordAmpCG(sti,2:8:end);
        Adat_compwindow = tracks_input(ti).tracksCoordAmpCG(sti,4:8:end);
 
-       trackmat_xyl(ti).xpos(sti,:) = [ repmat(NaN,[1 , (comptrack_birth-1)]), xdat_compwindow, repmat(NaN,[1 , comptrack_death_lag]) ];
-       trackmat_xyl(ti).ypos(sti,:) = [ repmat(NaN,[1 , (comptrack_birth-1)]), ydat_compwindow, repmat(NaN,[1 , comptrack_death_lag]) ];
-       trackmat_xyl(ti).Lamp(sti,:) = [ repmat(NaN,[1 , (comptrack_birth-1)]), Adat_compwindow, repmat(NaN,[1 , comptrack_death_lag]) ];
+       trackdat_xyl(ti).xpos(sti,:) = [ repmat(NaN,[1 , (comptrack_birth-1)]), xdat_compwindow, repmat(NaN,[1 , comptrack_death_lag]) ];
+       trackdat_xyl(ti).ypos(sti,:) = [ repmat(NaN,[1 , (comptrack_birth-1)]), ydat_compwindow, repmat(NaN,[1 , comptrack_death_lag]) ];
+       trackdat_xyl(ti).Lamp(sti,:) = [ repmat(NaN,[1 , (comptrack_birth-1)]), Adat_compwindow, repmat(NaN,[1 , comptrack_death_lag]) ];
 
     end % terminate forloop through subtracks
 
-    if(  ~all(  size( trackmat_xyl(ti).xpos ) == [ Nsubtracks(ti), Nframes] ) ||  ~all(  size( trackmat_xyl(ti).ypos ) == [ Nsubtracks(ti), Nframes] ) )
-       disp("unexpected dimension in trackmat_xyl.")
+    if(  ~all(  size( trackdat_xyl(ti).xpos ) == [ Nsubtracks(ti), Nframes] ) ||  ~all(  size( trackdat_xyl(ti).ypos ) == [ Nsubtracks(ti), Nframes] ) )
+       disp("unexpected dimension in trackdat_xyl.")
        return
     end
 
-    trackmat_xyl(ti).dx  = diff ( trackmat_xyl(ti).xpos, 1, 2 );
-    trackmat_xyl(ti).dy  = diff ( trackmat_xyl(ti).ypos, 1, 2 );
+    trackdat_xyl(ti).dx  = diff ( trackdat_xyl(ti).xpos, 1, 2 );
+    trackdat_xyl(ti).dy  = diff ( trackdat_xyl(ti).ypos, 1, 2 );
 
-    if(  ~all (  size( trackmat_xyl(ti).Lamp ) ==  [ Nsubtracks(ti), Nframes] ) )
-        disp("unexpected dimension in trackmat_xyl.Lamp.")
+    if(  ~all (  size( trackdat_xyl(ti).Lamp ) ==  [ Nsubtracks(ti), Nframes] ) )
+        disp("unexpected dimension in trackdat_xyl.Lamp.")
         return
     end
 

get_diffdat.m

@@ -10,7 +10,6 @@
 dout.y          = [];
 dndnp1          = [];
 
-
 % -------------------------------------------------
 % ---- First collect Diffdat for each polymer state
 
@@ -26,7 +25,7 @@
 
     % this is the diffusion constant, using the formula from Eq. 14 (page 022726-7
     % from Vestergaard et al, Phys. Rev. E. 89, (2014)
-    Diffdat{S}.D       = (dx2_ave/2*(dt)) + (dxndxnp1_ave/dt)/dt;
+    Diffdat{S}.D       = (dx2_ave/2*(dt)) + (dxndxnp1_ave/dt);
     Diffdat{S}.sigma2  = R*(dx2_ave) + (2*R-1)*dxndxnp1_ave;
 
     if( Diffdat{S}.sigma2 <1  )

get_state_lifetimes.m

@@ -1,6 +1,5 @@
-function [ state_lifetime_list ] =  get_state_lifetimes ( tracks_input, state_matrices_allti, max_state , Nframes )
-% Added on boztower at 21:50 on 25.10.2018
-%
+function [ state_lifetime_list ] =  get_state_lifetimes ( tracks_input, state_matrices_allti, max_state, dt, Nframes )
+% Calculations the number of intervening frames within dimerization events.
 
 Num_comp_tracks     = length( tracks_input );
 for s= 1:max_state
@@ -74,7 +73,7 @@
                 index = indices_right_shape(j);
                 [ state_this_window, excit_duration ]  = get_state( state_matrices_allti{ti}(sti,:), Events_this_track(index,:), Events_this_track(index+1,:) );
                 %                                                           ^merger event^     ,     ^split event^
-                state_lifetime_list{state_this_window} = [ state_lifetime_list{state_this_window}, excit_duration ] ;
+                state_lifetime_list{state_this_window} = [ state_lifetime_list{state_this_window}, dt * excit_duration ] ;
             end
         end
      end

master.m

@@ -1,11 +1,29 @@
-load("workspace_just_tracksFinal.mat")
-dt    = 0.04;
-Label = "DATANAME";
+% polytracker ---a software package for processing data from TIRF fluorescance 
+% videos
+% Copyright © 2017 Bren Osberg <[email protected]>
 
-R     = 1/6
+% ---- master file to run the polytracker software. You should be able 
+% to hit ctrl+Enter through the commands here after loading your tracksFinal data
+% structure into the workspace 
 
-% import tracksFinal, somehow,
-% then run this command:
+%% ==========================================================================
+%% 
+% ---- DEFINE VARIABLES RELEVANT TO THIS DATASET
 
-[ life, dens, lumen, Diffdat_p, D_observations] = polytrack( tracksFinal, Label, dt, R);
+dt         = 0.04;       %--- time spacing between frames
+px_spacing = 0.01066;    %--- pixel spacing (assuming tracksFinal stores position
+                         %    coordinates in units of pixels, this factor converts 
+                         %    the spatial dimension into micrometers.
+R          = 1/6;        %--- the motion blur constant, as defined in Vestergaard et 
+                         %    al, Phys. Rev. E. 89, (2014). Assuming the camera  
+                         %    shutter is left on continuously      
+
+Label      = "DATANAME"; %--- Some descriptive name for your dataset.
+
+Nbin       = 100;        %--- Resolution (number of bins) for your histograms. 
+
+%% ==========================================================================
+%% Now run the script: 
+
+[ life, dens, lumen, Diffdat_p, D_observations] = polytrack( tracksFinal, Label, dt, px_spacing, R, Nbin);
 

polytrack.m

@@ -1,9 +1,8 @@
 % take TracksFinal type data structure and dt spacing and some label, and
 % output relevant plots
 
-function [ lifetime_list, density, lumen_list,  Diffdat_p, D_observations] =  polytrack ( tracks_input_RAW, Label, dt , R )
+function [ lifetime_list, density, lumen_list,  Diffdat_p, D_observations] =  polytrack ( tracks_input_RAW, Label, dt, px_spacing, R, Nbin)
 
-RES = 100;
 % ===================================================
 % dat_in = "E:\NikonTIRF\04-10-18\beta1\141\TrackingPackage\tracks\Channel_1_tracking_result"
 % tracksoftware = "C:\u-track\software\plotCompTrack.m"
@@ -23,7 +22,7 @@
 %%  ===================================================
 % --- get xy-, dxdy-, and lumen data for each subtrack
 
-trackdat_xyl =  build_xyl_trackmat ( tracks_input, Nframes );
+trackdat_xyl =  build_xyl_trackdat ( tracks_input, px_spacing, Nframes );
 
 %%  ===================================================
 % --- Assign polymer state for each time point along each track:
@@ -36,9 +35,7 @@
 % Lifetime_list{1} is the list of lifetime observations for polymers in the 1 state
 % Lifetime_list{2} "" "" in the 2 state, etc.
 
-lifetime_list = get_state_lifetimes ( tracks_input, state_matrices_allti, max_state, Nframes );
-
-%%
+lifetime_list = get_state_lifetimes ( tracks_input, state_matrices_allti, max_state, dt, Nframes );
 
 all_lives_matter = [];
 
@@ -49,7 +46,7 @@
 
 figure(1)
 hist(all_lives_matter, 50)
-xlabel("# frames")
+xlabel(" lifetime [s]")
 ylabel("frequency")
 title( strcat('Merger liftime distribution; dataset: ', Label) )
 
@@ -95,13 +92,13 @@
 
 figure(6)
 subplot(2,1,1);
-hist(lumen_list{1}, RES)
+hist(lumen_list{1}, Nbin)
 xlabel("Intensity")
 ylabel("Freq")
 title( strcat('spectral distribution of monomers; dataset: ', Label) )
 
 subplot(2,1,2);
-hist(lumen_list{2}, RES)
+hist(lumen_list{2}, Nbin)
 xlabel("Intensity")
 ylabel("Freq")
 title( strcat('spectral distribution of dimers; dataset: ', Label) )
@@ -121,14 +118,14 @@
 title( strcat('position change -scatter') );
 
 subplot(2,1,2);
-hist(dndnp1, 2*RES);
+hist(dndnp1, 2*Nbin);
 xlim([-5, 5]);
 xlabel("dx_n * dx_{n+1}");
 ylabel("Freq");
 title( strcat('Two-frame drift correlation: ', Label) );
 
 figure(8);
-hist(D_observations, 2*RES);
+hist(D_observations, 2*Nbin);
 xlabel("Observed diffusion constant");
 ylabel("Freq");
 title( strcat('Diffusion constant calculation (like in PNAS 2013): ', Label) );

purge_ephemeral.m

@@ -33,4 +33,4 @@
 
   % (nothing with _RAW should be touched after this point )
 
-  end
+  end