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adding demos
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@tCeZ
tCeZ committed Mar 17, 2021
1 parent bb04462 commit 968f80c
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76 changes: 76 additions & 0 deletions demos/2D/demo2D00/demo2D00.m
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function answer = demo2D00( option )
% demo2D00
%
% Synthesize one 2D image with nuclear, cell shape, and vesicular channels
% from all vesicular object models (nucleoli, lysosomes, endosomes, and
% mitochondria) without convolution. The model was trained from the Murphy
% Lab 2D HeLa dataset.
%
% Input
% -----
% * a list of valid CellOrganizer model files
%
% Output
% ------
% * one TIFF file with six slices (nuclear, cell shape, nucleolar,
% lysosomal, endosomal, and mitochondrial channels)

% Ivan E. Cao-Berg (icaoberg@cmu.edu)
%
% Copyright (C) 2012-2019 Murphy Lab
% Computational Biology Department
% School of Computer Science
% Carnegie Mellon University
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published
% by the Free Software Foundation; either version 2 of the License,
% or (at your option) any later version.
%
% This program is distributed in the hope that it will be useful, but
% WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
% 02110-1301, USA.
%
% For additional information visit http://murphylab.web.cmu.edu or
% send email to murphy@cmu.edu

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% DO NOT MODIFY THIS BLOCK
if ~isdeployed()
current_path = which(mfilename);
[current_path, filename, extension] = fileparts( current_path );
cd(current_path);
end

disp( 'demo2D00' );

options.seed = 12345;
try
state = rng( options.seed );
catch err
rand( 'seed', options.seed ); %#ok<RAND>
end

options.targetDirectory = pwd;
options.prefix = 'imgs';
options.compression = 'lzw';
options.debug = false;
options.temporary_results = [ pwd filesep 'temporary_results' ];
options.verbose = false;
options.synthesis = 'all';
options.output.tifimages = false;
options.output.OMETIFF = true;
options.numberOfSynthesizedImages = 1;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

answer = slml2img( {'../../../models/2D/nucleolus.mat', ...
'../../../models/2D/lysosome.mat', ...
'../../../models/2D/endosome.mat', ...
'../../../models/2D/mitochondrion.mat'}, options );
end%demo2D00
93 changes: 93 additions & 0 deletions demos/2D/demo2D01/demo2D01.m
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function answer = demo2D01( options )
% demo2D01
%
% Train a 2D generative model of the nucleus, cell shape, and lysosomes using
% all LAMP2 images in the Murphy Lab 2D HeLa dataset.
%
% Input
% -----
% * a directory of raw or synthetic nucleus images
% * a directory of raw or synthetic cell shape images
% * a directory of raw or synthetic lysosome images
% * the resolution of the images (all images should have the same
% resolution)
%
% Output
% ------
% * a valid SLML model file

% Ivan E. Cao-Berg (icaoberg@cmu.edu)
%
% Copyright (C) 2013-2020 Murphy Lab
% Computational Biology Department
% School of Computer Science
% Carnegie Mellon University
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published
% by the Free Software Foundation; either version 2 of the License,
% or (at your option) any later version.
%
% This program is distributed in the hope that it will be useful, but
% WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
% 02110-1301, USA.
%
% For additional information visit http://murphylab.web.cmu.edu or
% send email to murphy@cmu.edu

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% DO NOT MODIFY THIS BLOCK
if ~isdeployed()
current_path = which(mfilename);
[current_path, filename, extension] = fileparts( current_path );
get_murphylab_image_collections( true );
cd(current_path);
end

disp( 'demo2D01' );
disp( 'The estimated running time is 7-10 minutes. Please wait.' );

options.verbose = true;
options.debug = true;
options.save_segmentations = true;
options.display = false;
options.skip_preprocessing = true;
options.model.name = 'demo2D01';
options = ml_initparam( options, struct( ...
'train', struct( 'flag', 'all' )));
options.nucleus.class = 'nuclear_membrane';
options.nucleus.type = 'medial_axis';
options.cell.class = 'cell_membrane';
options.cell.type = 'ratio';
options.protein.class = 'vesicle';
options.save_segmentations = true;
options.protein.type = 'gmm';
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

dna = {}; cellm = {}; protein = {}; options.masks = {}; options.labels = {};

directory = '../../../images/HeLa/2D/LAM';
for i=1:1:25
dna{length(dna)+1} = [ directory filesep 'orgdna' filesep 'cell' num2str(i) '.tif' ];
cellm{length(cellm)+1} = [ directory filesep 'orgcell' filesep 'cell' num2str(i) '.tif' ];
protein{length(protein)+1} = [ directory filesep 'orgprot' filesep 'cell' num2str(i) '.tif' ];
options.labels{length(options.labels)+1} = 'LAMP2';
options.masks{length(options.masks)+1} = [ directory filesep 'crop' filesep 'cell' num2str(i) '.tif' ];
end

options.temporary_results = [ pwd filesep 'temporary_results' ];
options.model.resolution = [ 0.049, 0.049 ];
options.model.filename = 'lamp2.xml';
options.model.id = 'lamp2';
options.model.name = 'lamp2';

%documentation
options.documentation.description = 'This model has been trained using demo2D01 from CellOrganizer';

answer = img2slml( '2D', dna, cellm, protein, options );
82 changes: 82 additions & 0 deletions demos/2D/demo2D02/demo2D02.m
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function answer = demo2D02()
% demo2D02
%
% Synthesize one 2D image with nuclear, cell shape, and lysosomal channels
% from LAMP2 model trained in demo2D01 without convolution.
%
% Input
% -----
% * a valid CellOrganizer model file
%
% Output
% ------
% * one TIFF file with three slices (nuclear, cell shape, and lysosomal
% channels)

% Ivan E. Cao-Berg (icaoberg@cmu.edu)
%
% Copyright (C) 2013-2018 Murphy Lab
% Computational Biology Department
% School of Computer Science
% Carnegie Mellon University
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published
% by the Free Software Foundation; either version 2 of the License,
% or (at your option) any later version.
%
% This program is distributed in the hope that it will be useful, but
% WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
% 02110-1301, USA.
%
% For additional information visit http://murphylab.web.cmu.edu or
% send email to murphy@cmu.edu

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% DO NOT MODIFY THIS BLOCK
if ~isdeployed()
current_path = which(mfilename);
[current_path, filename, extension] = fileparts( current_path );
cd(current_path);
end

disp( 'demo2D02' );
disp( 'The estimated running time is 1 minute. Please wait.' );

options.seed = 12345;
try
state = rng( options.seed );
catch err
rand( 'seed', options.seed ); %#ok<RAND>
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%modify the next line to generate more images
options.numberOfSynthesizedImages = 1;

options.targetDirectory = pwd;
options.prefix = 'img';
options.compression = 'lzw';
options.debug = false;
options.verbose = true;
options.display = false;

filename = '../demo2D01/lamp2.mat';
if ~exist( filename )
warning( [ 'File ' filename ' not found.' ] );
disp('Using alternative model present in this distribution.');
filename = '../../../models/2D/endosome.mat';
end

options.output.tifimages = false;
options.output.OMETIFF = true;

slml2img( {filename}, options );
answer = true;
end%demo2D02
85 changes: 85 additions & 0 deletions demos/2D/demo2D03/demo2D03.m
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function answer = demo2D03(options)
% demo2D03
%
% Train 2D generative model of the nucleus and cell shape using
% all LAMP2 images in the Murphy Lab 2D HeLa dataset.
%
% Input
% -----
% * a directory of raw or synthetic nucleus images
% * a directory of raw or synthetic cell shape images
% * the resolution of the images (all images should have the same
% resolution)
%
% Output
% ------
% * a valid SLML model file

% Ivan E. Cao-Berg (icaoberg@cmu.edu)
%
% Copyright (C) 2015-2019 Murphy Lab
% Computational Biology Department
% School of Computer Science
% Carnegie Mellon University
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published
% by the Free Software Foundation; either version 2 of the License,
% or (at your option) any later version.
%
% This program is distributed in the hope that it will be useful, but
% WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
% 02110-1301, USA.
%
% For additional information visit http://murphylab.web.cmu.edu or
% send email to murphy@cmu.edu

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% DO NOT MODIFY THIS BLOCK
if ~isdeployed()
current_path = which(mfilename);
[current_path, filename, extension] = fileparts( current_path );
get_murphylab_image_collections( true );
cd(current_path);
end

disp( 'demo2D03' );
warning('This demo is deprecated. The demo will be removed in future versions of CellOrganizer');
disp( 'The estimated running time is 9 minutes. Please wait.' );

options.verbose = true;
options.debug = true;
options.display = false;
options.model.name = 'demo2D03';
options = ml_initparam( options, struct( ...
'train', struct( 'flag', 'framework' )));
options.nucleus.class = 'nuclear_membrane';
options.nucleus.type = 'medial_axis';
options.cell.class = 'cell_membrane';
options.cell.type = 'ratio';
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% the following list of parameters are adapted to the LAMP2 image
% collection, modify these according to your needs
directory = '../../../images/HeLa/2D/LAM/';
dna = {}; cellm = {}; protein = {}; options.masks = {};
for i=1:1:25
dna{length(dna)+1} = [ directory filesep 'orgdna' filesep 'cell' num2str(i) '.tif' ];
cellm{length(cellm)+1} = [ directory filesep 'orgcell' filesep 'cell' num2str(i) '.tif' ];
options.masks{length(options.masks)+1} = [ directory filesep 'crop' filesep 'cell' num2str(i) '.tif' ];
end

options.model.resolution = [ 0.049, 0.049 ];
options.model.filename = 'lamp2.xml';
options.model.id = 'lamp2';

%documentation
options.documentation.description = 'This model has been trained using demo2D0333 from CellOrganizer';

answer = img2slml( '2D', dna, cellm, protein, options );
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