Repair AxonSeg

AxonSeg.m

@@ -15,10 +15,10 @@
 % ----------------------------------------------------------------------------------------------------
 % Example:
 %   Segment and generate a SegParameters.mat file:
-%     AxonSeg test_image_OM_crop.tif
+%     AxonSeg test_image_OM_2.tif
 %
 %   Segment a new image using the same SegParameters:
-%     AxonSeg test_image_2.tif SegParameters.mat -nogui
+%     AxonSeg test_image_OM_2.tif SegParameters.mat -nogui
 %
 %   Segment myelin using a corrected axon mask:
 %     AxonSeg({'RawImage.tif','Seg_mask_axon_corr.tif'}, 'SegParameters.mat', '-nogui')

code/Blockprocessing/as_listcell2axonlist.m

@@ -27,7 +27,7 @@
 % list of cell 2 one list only
 axonlist(length(listcell_seg))=listcell_seg{end};
 [axonlist.seg]=deal(listcell_seg{:});
-axonlist=cat(2,axonlist.seg); axonlist=cat(2,axonlist.seg); axonlist=axonlist(logical([axonlist.myelinAera])); % weird but works (fast).. keep everything
+axonlist=cat(2,axonlist.seg); axonlist=cat(2,axonlist.seg); axonlist=axonlist(logical([axonlist.gRatio])); % weird but works (fast).. keep everything
 
 % remove axons that have been segmented twice
 centroids=cat(1,axonlist.Centroid);

code/Seg_myelin/as_myelinseg2axonlist.m

@@ -10,16 +10,13 @@
 for iaxon=size(seg,3):-1:1
     [axonlist(iaxon).data(:,1), axonlist(iaxon).data(:,2)]=find(seg(:,:,iaxon));
     axonlist(iaxon).data = single(axonlist(iaxon).data);
-    axonlist(iaxon).myelinAera=size(axonlist(iaxon).data,1);
-    axonlist(iaxon).axonID=repmat(iaxon,[axonlist(iaxon).myelinAera,1]);
     tmp=regionprops(seg(:,:,iaxon),'Centroid');
     if isempty(tmp), axonlist(iaxon).Centroid=[];
     else
-            axonlist(iaxon).Centroid=tmp(1).Centroid([2 1]);
+        axonlist(iaxon).Centroid=tmp(1).Centroid([2 1]);
     end
     for istat=1:length(sfields)
         tmp=stats.(sfields{istat});
         axonlist(iaxon).(sfields{istat})=tmp(iaxon);
     end
 end
-

code/Seg_myelin/as_stats.m

@@ -1,45 +1,45 @@
-function AXstat =as_stats(bwseg,PixelSize,myelin,metric)
-% statis=as_stats(bwseg,pixelSize,myelin)
+function AXstat =as_stats(myelinseg,pixelSize,myelin)
+% AXstat=as_stats(myelinseg,pixelSize)
 if ~exist('myelin','var'), myelin=1; end
 
 
-bwseg=reshape2D(~~bwseg,1);
-Npix = length(bwseg(:));
-cc = bwconncomp(bwseg, 8);
-if myelin
-    myelinseg = bwseg;
-    bwseg = logical(imfill(myelinseg,'holes') - myelinseg);
-end
-
-stats                   =   regionprops(bwseg,{'Eccentricity', 'EquivDiameter','Area'});
+myelinseg=reshape2D(myelinseg,1);
+cc = bwconncomp(myelinseg, 8);
+prop =regionprops(cc, {'Area', 'FilledArea'});
 
-% convert units pixel to meters
-EquivDiameter = [stats.EquivDiameter]*PixelSize;
+% Creation of a struct var for the stats
+AXstat=struct('axonEquivDiameter',0,'gRatio',0,'myelinThickness',0);
 
-AXstat.EquivDiameter01   =   sum(EquivDiameter>0 & EquivDiameter<1);
-AXstat.EquivDiameter14   =   sum(EquivDiameter>1 & EquivDiameter<4);
-AXstat.EquivDiameter48   =   sum(EquivDiameter>4 & EquivDiameter<8);
-AXstat.EquivDiameter812  =   sum(EquivDiameter>8 & EquivDiameter<12);
-AXstat.EquivDiameter1217  =   sum(EquivDiameter>12 & EquivDiameter<17);
-AXstat.EquivDiameter     =   mean(EquivDiameter);
-AXstat.EquivDiameter_W   =   sum(EquivDiameter.^3)/sum(EquivDiameter.^2);
-AXstat.EquivDiameter_std =   std(EquivDiameter);
-AXstat.Eccentricity      =   max([stats.Eccentricity]);
-AXstat.AVF               =   sum([stats.Area])/Npix;
-AXstat.Naxons            =   length(stats);
 
-if myelin
-    stats                   =   regionprops(myelinseg,{'EquivDiameter'});
-    myelinEquivDiameter = [stats.EquivDiameter]*PixelSize;
-    AXstat.MVF = sum(myelinseg)/Npix;
-    AXstat.myelinEquivDiameter = median(myelinEquivDiameter);
-    try
-    AXstat.gRatio = single(EquivDiameter ./ myelinEquivDiameter);
-    catch
-        warning('Some myelin have no holes')
+if ~isempty(prop)
+    % Area gives myelin area & FilledArea gives (myelin+axon) area
+    area = [[prop.Area]' [prop.FilledArea]'-[prop.Area]'];
+    % Calculate myelin area by using pixel size
+    if myelin
+        myelinArea = single(area(:, 1).*pixelSize^2);
+    end
+    % Calculate axon area by using pixel size
+    if myelin
+        axonArea = single(area(:, 2).*pixelSize^2);
+    else
+        axonArea = single(area(:, 1).*pixelSize^2);
+    end
+    % Myelin equiv. diameter = sqrt(4*TotalArea/pi)
+    if myelin
+        myelinEquivDiameter = single(sqrt(4*(myelinArea + axonArea)/pi));
     end
+    % Axon equiv. diameter = sqrt(4*AxonArea/pi)
+    AXstat.axonEquivDiameter = single(sqrt(4*axonArea/pi));
+    % Calculate gRatio
+    if myelin
+        AXstat.gRatio = single(AXstat.axonEquivDiameter ./ myelinEquivDiameter);
+        % Myelin thickness = (MyelinDiam - AxonDiam)/2
+        AXstat.myelinThickness = single((myelinEquivDiameter - AXstat.axonEquivDiameter) / 2);
+    end
+
+    %     if nargout>0
+    %         MorphoStat.circularity=;
+    %     end
 end
 
-if exist('metric','var')
-    AXstat = AXstat.(metric);
-end
+

code/Stats/as_stats_fields.m

@@ -1,6 +1,3 @@
-function fields=as_stats_fields
+function fieldsval=as_stats_fields
 
-fields={...
-    'gRatio'...
-    'axonEquivDiameter'...
-    'myelinThickness'};
+fieldsval=fields(as_stats([1 1; 1 1],1));

code/axonlist/as_display_label.m

@@ -35,7 +35,7 @@
 for i=Naxon:-1:1
     if ~mod(i,1000), disp(i); end
     if size(axonlist(i).data,1)>5
-        index=round(double(axonlist(i).data)+repmat(axonlist(i).Centroid,[size(axonlist(i).data,1),1]));
+        index=round(double(axonlist(i).data));
 
         %   If 'axon' display type is specified, find axon index instead of
         %   myelin index

code/batch_multiple_segmentations.m

@@ -44,14 +44,14 @@
 % imshow(display_1);
 
 maxdiam=ceil(prctile(cat(1,axonlist.axonEquivDiameter),99));
-imwrite(display_1,[output 'axonEquivDiameter_(axons)_0µm_' num2str(maxdiam) 'µm.jpg'])
+imwrite(display_1,[output 'axonEquivDiameter_(axons)_0um_' num2str(maxdiam) 'um.jpg'])
 
 
 %%
 
 % reduce size of axonlist - eliminate all unecessary fields
 
-fields_to_remove = {'data','axonID'}; % erasing these 2 fields reduces axonlist size by 90% 1 MB -> 113 KB for example
+fields_to_remove = {'data'}; % erasing these 2 fields reduces axonlist size by 90% 1 MB -> 113 KB for example
 axonlist_reduced=rmfield(axonlist,fields_to_remove);
 % save('axonlist_reduced.mat','axonlist_reduced','-v7.3');
 

code/imageprocessing/as_improc_blockwising.m

@@ -24,7 +24,7 @@
     end
 end
 
-parfor(block=1:n_blocki*n_blockj,parforArg)
+for (block=1:n_blocki*n_blockj)
     j=1+(blocksize-overlap)*(mod(block-1,n_blockj));
     i=1+(blocksize-overlap)*(block-mod(block-1,n_blockj)-1)/n_blockj;