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IAH public
DeProj
Commits
87573e8f
Commit
87573e8f
authored
Jul 26, 2020
by
Jean-Yves TINEVEZ
Browse files
Example import of the bellaiche file format + mesh.
parent
46e25fde
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RunExample2.m
0 → 100755
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87573e8f
%% 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
);
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