subscript of Persistencelength_full.m

Amira_lineset_conversion.m

@@ -0,0 +1,102 @@
+%% Amira_lineset_conversion
+
+
+% Felix JB Baeuerlein
+
+% Baeuerlein et al. Cell 2017
+
+%% script body
+
+% procedure to convert new Amira 6.0.1 Filament Tracing Data into the 
+% Amira 5.4.0 format:
+% filaments (:,1) = point index (from 0 to the last index, 1 index per point, independently of the line number)
+% filaments (:,2) = coord X of the point
+% filaments (:,3) = coord Y of the point
+% filaments (:,4) = coord Z of the point
+% filaments (:,5) = line index (start with 0)
+% filaments (:,6) = point index along a line (restart to 0 for each new line)
+% filaments (:,7) = CC
+% filaments (:,8) = Sim
+% filaments (:,9) = theta (from the Y-axis to the X-axis, range: 0 .. 180)
+% filaments (:,10) = psi (angle from the XY plane to the Z, range: 0..90)
+% filaments (:,11) = line length
+
+% Load data
+[filename, pathname] = uigetfile({'*.xlsx'},'File Selector');
+% filename='t79_C70_L40_S50.attributegraph.xlsx';
+[~, ~, Seg] = xlsread([pathname filename],'Segments');
+[~, ~, Points] = xlsread([pathname filename],'Points');
+
+N = 2; % counter for Segment-file line
+L = 10; % if Amiradata in ? - to convert to nm
+
+
+for i= 2:length(Points)
+
+    if N < length(Seg)-1
+            if min(str2num(Seg{N+1,10})) == i-2
+                N=N+1;
+            end
+            else
+                N=length(Seg)-1;
+    end
+
+    if N < length(Seg)-1
+            if Points{i,1} < min(str2num(Seg{N+1,10}))
+                Points{i,2} = Points{i,2}./L; % conversion of Lengthes defined in Amira to nm
+                Points{i,3} = Points{i,3}./L; % conversion of Lengthes defined in Amira to nm
+                Points{i,4} = Points{i,4}./L; % conversion of Lengthes defined in Amira to nm
+                Points{i,5}=Seg{N,7}; % line index (start with 0)
+                Points{i,6}=Points{i,1}-(min(str2num(Seg{N,10}))-1); % point index
+                Points{i,7}=0;
+                Points{i,8}=0;
+                Points{i,9}=Seg{N,5}; % theta (from the Y-axis to the X-axis, range: 0 .. 180)
+                Points{i,10}=Seg{N,6}; % psi (angle from the XY plane to the Z, range: 0..90)
+                Points{i,11}=Seg{N,2}./L; % line length
+            end
+    else
+                Points{i,2} = Points{i,2}/L; % conversion of Lengthes defined in Amira to nm
+                Points{i,3} = Points{i,3}/L; % conversion of Lengthes defined in Amira to nm
+                Points{i,4} = Points{i,4}/L; % conversion of Lengthes defined in Amira to nm
+                Points{i,5}=Seg{N,7}; % line index (start with 0)
+                Points{i,6}=Points{i,1}-(min(str2num(Seg{N,10}))-1); % point index
+                Points{i,7}=0;
+                Points{i,8}=0;
+                Points{i,9}=Seg{N,5}; % theta (from the Y-axis to the X-axis, range: 0 .. 180)
+                Points{i,10}=Seg{N,6}; % psi (angle from the XY plane to the Z, range: 0..90)
+                Points{i,11}=Seg{N,2}./L; % line length
+    end
+
+end
+
+
+Points=cell2mat(Points(2:length(Points),:));
+csvwrite([filename '_Points.csv'], Points)
+
+Line=cell2mat(Seg(2:end,1:9));
+Line2(:,1)=Line(:,1);
+Line2(:,2)=Line(:,2)/10;
+Line2(:,3:4)=Line(:,5:6);
+Line2(:,5)=ones(length(Line2),1)*85;
+csvwrite([filename '_Lines.csv'], Line2)
+
+
+% % visualizes the first 50 filaments
+% for ff=0:50
+%     ind = find(Points(:,5) == ff); 
+%     plot3(Points(ind,2), Points(ind,3), Points(ind,4), '*-');
+%     axis equal
+%     view([-35.5 14]);
+%     box('on');
+%     grid('on');
+%     xlabel('x');
+%     ylabel('y');
+%     zlabel('z');
+%   %  legend(ind, '# Filament')
+%     pause(0.2)
+%     hold on
+%     ind = find(filaments(:,5) == ff); 
+%     plot3(filaments(ind,2), filaments(ind,3), filaments(ind,4), 'or');
+%     pause(0.5)
+%     hold off
+% end