Example import of the bellaiche file format + mesh.

RunExample2.m

+%% Example de-projection script, using a cell result structure and a mesh.
+
+%% 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';
+
+% The segmentation results. Here we use the results from Y. Bellaiche lab
+% analysis software. The results must contain a CELL, FRAME, VERTICES and
+% SIDES structures.
+segmentation_filename   = 'SIA_161210_gfapnlsg_Backup_001.mat';
+
+% The tissue surface mesh. It must be a mesh mapping the tissue surface, 
+% openedd at the tissue borders.
+mesh_filename           = 'SimplifiedMesh.ply';
+
+% The physical unit of length must be specified (not stored elsewhere).
+units = 'µm';
+
+%% Read files.
+
+% Segmentation results.
+fprintf('Opening segmentation file: %s\n', segmentation_filename )
+seg = load( fullfile( root_folder, segmentation_filename ) );
+
+% Path to mesh file.
+mesh_file_path = fullfile( root_folder, mesh_filename );
+
+%% Create deproj instance.
+
+dpr = deproj.from_bellaiche( ...
+    seg.CELLS, ...
+    seg.FRAME, ...
+    seg.SIDES, ...
+    seg.VERTICES, ...
+    mesh_file_path, ...
+    units  );
+
+%% Plot morphological parameters.
+
+close all
+plot_sizes( dpr );
+plot_fit_plane( dpr );
+plot_fit_ellipse( dpr );
+plot_curvatures( dpr );
+plot_distorsions( dpr );