Commit 3a6f69f5 authored by Jean-Yves TINEVEZ's avatar Jean-Yves TINEVEZ
Browse files

Better comments for example 4.

parent 3f2fe7b5
%% Display an image on the tissue surface.
% We take the same data than for the first example and regenerate the
% deproj object for it.
%
% Then we plot the segmentation results (in 3D) and map the image of the 2D
% projection image on the tissue surface.
%% Clear all.
......@@ -8,47 +14,17 @@ clc
%% Parameters, scripts and files location.
% Add DeProj functions to the path.
% Same things that for example 1. I will skip comments.
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.
......@@ -72,20 +48,33 @@ dpr = deproj.from_heightmap( ...
inpaint_zeros, ...
prune_zeros );
%% Load the image to map.
close all
%% Load the image to map and display it.
% The image to display must be a 2D image, colored of grayscale. Ideally it
% has the same number of pixels and the same pixel size that the
% segmentation image that helped creating the deproj object.
% What really matter is that we can have share X,Y coordinates thanks to
% the pixel size and origin of the image.
fprintf('Opening the image to map: %s\n', image_file_path )
% Since it is a color image, we also load the LUT in the Tmap variable.
[ T, Tmap ] = imread( image_file_path );
figure
hold on
axis equal
% Plot the segmentation. If we pass 'w' to the 'plot_values_contour', the
% cell faces will be transparent and their border will be painted in white.
hc = dpr.plot_values_contour( 'w', gca );
hc.LineWidth = 1;
% This is the the command to plot the image on the tissue surface. Since we
% have a color image, we pass the 'Tmap' array that contains the LUT of the
% image. If you have a grayscale image, just pass the empty array [].
dpr.texture_image( T, Tmap, pixel_size );
% Put some lighting and orientation so that we can get a feeling of the
% tissue ripples.
axis off
lighting gouraud
light
......
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