Example texturing an image on the drosophila sample.

RunExample4.m

+%% Display an image on the tissue surface.
+
+%% Clear all.
+
+close all
+clear
+clc
+
+%% Parameters, scripts and files location.
+
+% Add DeProj functions to the path.
+addpath('./src')
+
+% Where are the images.
+root_folder = 'samples';
+
+% You can provide directly the segmentation results as a mask image, and
+% the code below will convert it into a list of objects.
+% For this to work, the mask image must be an 'ImageJ' mask, that is: the
+% cell contours must be black (pixel value == 0) and the cell interiors
+% must be white (pixel value > 0).
+mask_filename       = 'Segmentation-2.tif';
+
+% The height-map is an image that stores at every pixel the location of the
+% plane of interest in the source 3D image. Since the pixel values store 
+% the index of the plane, we will need to convert it to an elevation in µm
+% (see the voxel_depth parameter below).
+heightmap_filename  = 'HeightMap-2.tif';
+
+% The image to map on the tissue surface. In this example we simply take
+% a capture of the projection results.
+image_file_path     = 'static/Projection-2.png';
+
+% Pixel XY size.
+% Physical size of a pixel in X and Y. This will be used to report sizes in
+% µm.
+pixel_size = 0.183; % µm
+units = 'µm';
+
+% Z spacing.
+% How many µm bewtween each Z-slices. We need this to convert the
+% height-map values, that stores the plane of interest, into µm.
+voxel_depth = 1.; % µm
+
+
+% Try to remove objects that have a Z position equal to 0. Normally this
+% value reports objects that are out of the region-of-interest.
+prune_zeros = true;
+inpaint_zeros = true;
+
+% Invert z for plotting.
+invert_z = true;
+
+%% Read files.
+
+% ImageJ mask.
+fprintf('Opening mask image: %s\n', mask_filename )
+I = imread( fullfile( root_folder, mask_filename ) );
+
+fprintf('Opening height-map image: %s\n', heightmap_filename )
+H = imread( fullfile( root_folder, heightmap_filename ) );
+
+%% Create deproj instance.
+
+dpr = deproj.from_heightmap( ...
+    I, ...
+    H, ...
+    pixel_size, ...
+    voxel_depth, ...
+    units, ...
+    invert_z, ...    
+    inpaint_zeros, ...
+    prune_zeros );
+
+%% Load the image to map.
+
+close all
+
+fprintf('Opening the image to map: %s\n', image_file_path )
+[ T, Tmap ] = imread( image_file_path );
+
+figure 
+hold on
+axis equal
+
+hc = dpr.plot_values_contour( 'w', gca );
+hc.LineWidth = 1;
+dpr.texture_image( T, Tmap, pixel_size );
+axis off
+lighting gouraud
+light
+
+el = 23;
+az = -73;
+view( az, el )
+axis tight
+
+title( 'Texturing the projection on the segmentation results.', ...
+    'FontWeight', 'normal', ...
+    'Interpreter', 'none' )