Clean the help

doc/batch_axonlist.m

@@ -10,13 +10,17 @@
 % Tutorial to manipulate axonlist structure
 
 
-%% PART 1 - LOAD SEGMENTATION RESULTS
+%% PART 1 - SEGMENT
+
+AxonSeg test_image_OM_2.tif SegParameters.mat -nogui
+
+%% PART 2 - LOAD SEGMENTATION RESULTS
 
 % load Segmentation Results (be patient.. can take some time)
-load('axonlist_full.mat');
+load('axonlist_full_image.mat');
 
 
-%% PART 2 - EXPLORE AXONLIST STRUCTURE FOR MORPHOMETRY ANALYSIS OF THE DATA
+%% PART 3 - EXPLORE AXONLIST STRUCTURE FOR MORPHOMETRY ANALYSIS OF THE DATA
 
 
 % number of axons segmented :
@@ -37,38 +41,19 @@
 % Calculate stats of distribution
 
 diam_mean=mean(Axon_diameters);
-disp(['mean axon diameter in this image is : ' num2str(diam_mean) ' µm'])
+disp(['mean axon diameter in this image is : ' num2str(diam_mean) ' ?m'])
 diam_std=std(Axon_diameters);
-disp(['axon diameter standard deviation in this image is : ' num2str(diam_std) ' µm'])
+disp(['axon diameter standard deviation in this image is : ' num2str(diam_std) ' ?m'])
 
 
-% Remove axons larger than 15 µm
+% Remove axons larger than 15 ?m
 axonlist_2=axonlist(Axon_diameters<9);
 nbaxons = length(axonlist_2);
-disp(['number of axons segmented (<9µm) : ' num2str(nbaxons) ' axons']);
-
-%% PART 2 - EXTRACT STATS OF A PARTICULAR ROI
-
-% Create a binary mask to extract stats
-
-mask=imread('mask_2.png');
-
-
-% Register mask on image (click each mask region in registration GUI)
-[mask_reg_labeled, P_color]=as_reg_mask(mask,img);
-
-% get indexes of axons in each region of the mask
-indexes=as_stats_mask_labeled(axonlist, mask_reg_labeled);
-
-% plot barplots for main stats
-as_stats_barplot(axonlist,indexes,P_color);
+disp(['number of axons segmented (<9?m) : ' num2str(nbaxons) ' axons']);
 
 
 
-
-%% PART 3 - EXPLORE AXON AND MYELIN DISPLAY OPTIONS AVAILABLE
-
-
+%% PART 2 - EXPLORE AXON AND MYELIN DISPLAY OPTIONS AVAILABLE
 
 % Produce an axon display colorcoded for axon diameter on initial gray
 % image
@@ -112,7 +97,7 @@
 
 % Save last display to current folder
 
-imwrite(display_1,'Axon_display.tif');
+imwrite(display_5,'Axon_display.tif');
 
 
 % Get the binary image of axon objects
@@ -134,46 +119,3 @@
 
 img_BW_fibers=im2bw(bw_axonseg_axons+bw_axonseg_myelins,0);
 imshow(img_BW_fibers);
-
-
-% Use fiber binary image as mask to select fibers in gray image
-
-
-fibers_extract=uint8(img_BW_fibers).*img;
-imshow(fibers_extract);
-% imwrite(fibers_extract,'fibers_masked.tif');
-
-
-%% WARP STATS FROM HISTOLOGY TO MRI
-
-% Downsample histology data
-
-as_stats_downsample_2nii(axonlist,size(img),PixelSize,150);
-
-
-
-
-
-
-
-
-%%
-
-% %% PART 1 - 
-% 
-% % calculate myelin volume fraction (MVF) in an image
-% 
-% total_area=size(img,1)*size(img,2);
-% 
-% bw_axonseg=as_display_label(axonlist,size(img),'axonEquivDiameter','myelin');
-% img_BW_myelins=im2bw(bw_axonseg,0);
-% 
-% myelin_area=sum(sum(img_BW_myelins));
-% 
-% MVF=myelin_area/total_area;
-% 
-% 
-
-
-
-