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pipeline_image_processing.m
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%
% creates 3D image stacks from tissuecyte sections
% and uses the ANTs image registration toolkit (https://stnava.github.io/ANTs/)
% to align them with the Allen template
% @ henrik.skibbe
%
function pipeline_image_processing(id)
%%
raw_folder='./data/raw/';
db_folder='./data/database/';
allen_ref_folder = './allen_avg/';
allen_ref = [allen_ref_folder,'/P56_Atlas.nii.gz'];
antsApply = './bin/antsApplyTransforms';
if ~(exist([raw_folder,id,'/meta/'],'dir')==7)
fprintf('META FILE MISSING -> SKIPPING\n');
return;
end
assert(exist([raw_folder,id,'/meta/'],'dir')==7);
do_3D = true;
compute_Transform = true;
apply_Transform = true;
map_atlas_to_org = true;
atlas_to_2D = true;
highres = true;
addpath helper_scripts
if do_3D
meta_folder = [db_folder,'/',id,'/meta/'];
mkdir(meta_folder);
metadata_folder = meta_folder;
trafo_file = [meta_folder,'trafo.mat'];
for channel = 1:4
ifolder=[db_folder,'/',id,'/2D/'];
ofolder=[db_folder,'/',id,'/3D/'];
mkdir([ofolder,'/c',num2str(channel),'/']);
make_my_nii = @(ifile,ofile,varargin)tissuecute_make_nii_mouse(ifile,ofile,varargin{:});
tissuecyte_stitch_3D_2020(ifolder,ofolder,channel,'element_size_xy',[50,50]/2,'metadata_folder',[metadata_folder,'../'],'trafo_file',trafo_file,'make_my_nii',make_my_nii,'ext','tif');
end
end
%%
if compute_Transform
%%
channel=1;
ofolder_ref =[db_folder,'/',id,'/3D/reg/'];
mkdir(ofolder_ref);
move=[db_folder,'/',id,'/3D/c',num2str(channel),'/img3D_raw_TC_org.nii.gz'];
out=[ofolder_ref,'/trafo.nii.gz'];
cmd = [ './reg_2_allen.sh',...
' ',move,...
' ',allen_ref,...
' ',out...
];
system(cmd)
end
if apply_Transform
%%
fnames = {};
for channel = 1:4
fnames{numel(fnames)+1}=[db_folder,'/',id,'/3D/c',num2str(channel),'/img3D_raw_TC_org.nii.gz'];
fnames{numel(fnames)+1}=[db_folder,'/',id,'/3D/c',num2str(channel),'/img3D_vis_TC_org.nii.gz'];
end
for f=1:numel(fnames)
%%
move = fnames{f};
trafo=[ofolder_ref,'/trafo.nii.gz'];
out=[move];
out = strrep(out,'.nii.gz','_to_allen.nii.gz');
out = strrep(out,[db_folder,'/',id,'/3D'],[db_folder,'/',id,'/3D/reg/']);
[filepath,name,ext] = fileparts(out);
mkdir(filepath);
cmd = [antsApply, ' ',...
' -i ',move,...
' -o ',out,...
' -r ',allen_ref...
' -n Linear --float 1 -v 1 -t ',trafo,'Composite.h5',...
];
system(cmd)
end
end
if map_atlas_to_org
ofolder_ref =[db_folder,'/',id,'/3D/reg/'];
ofolder = [ofolder_ref,'/allen/'];
mkdir(ofolder);
fname = 'P56_Atlas.nii.gz';
out=[ofolder,fname];
channel = 1;
move= [allen_ref_folder,fname];
fix = [db_folder,'/',id,'/3D/c',num2str(channel),'/img3D_raw_TC_org.nii.gz'];
trafo=[ofolder_ref,'/trafo.nii.gz'];
[filepath,name,ext] = fileparts(out);
mkdir(filepath);
cmd = [antsApply, ' ',...
' -i ',move,...
' -o ',out,...
' -r ',fix...
' -n Linear --float 1 -v 1 -t ',trafo,'InverseComposite.h5',...
];
system(cmd)
fname = 'P56_Annotation.nii.gz';
out=[ofolder,fname];
channel = 1;
move= [allen_ref_folder,fname];
fix = [db_folder,'/',id,'/3D/c',num2str(channel),'/img3D_raw_TC_org.nii.gz'];
trafo=[ofolder_ref,'/trafo.nii.gz'];
[filepath,name,ext] = fileparts(out);
mkdir(filepath);
cmd = [ antsApply,' ',...
' -i ',move,...
' -o ',out,...
' -r ',fix...
' -n MultiLabel --float 1 -v 1 -t ',trafo,'InverseComposite.h5',...
];
system(cmd)
end
if atlas_to_2D
addpath /disk/k_raid/KAKUSHIN-NOU-DATA/SOFT/pipeline/skibbe-h_rep/matlab/
ofolder_base =[db_folder,'/',id,'/2D/allen/'];
ifolder_ref =[db_folder,'/',id,'/3D/reg/'];
ifolder = [ifolder_ref,'/allen/'];
if true
fname = 'P56_Atlas.nii.gz';
ifile = [ifolder,fname];
ofolder = [ofolder_base,strrep(fname,'.nii.gz','/')];
mkdir(ofolder)
pipeline_nifit_2_slice(...
'ifile',ifile,...
'ofolder',ofolder,...
'isatlas',false);
end
fname = 'P56_Annotation.nii.gz';
ifile = [ifolder,fname];
ofolder = [ofolder_base,strrep(fname,'.nii.gz','/')];
mkdir(ofolder)
pipeline_nifit_2_slice(...
'ifile',ifile,...
'ofolder',ofolder,...
'isatlas',true,'landmarks',true);
end
if highres
tissuecute_Nagai_slice_map_to_slice_Allen_std(id,'c1','tif');
tissuecute_Nagai_slice_map_to_slice_Allen_std(id,'c2','tif');
tissuecute_Nagai_slice_map_to_slice_Allen_std(id,'c3','tif');
tissuecute_Nagai_slice_map_to_slice_Allen_std(id,'c4','tif');
end