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STEP_5_Transform_and_ROI_drawing.m
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STEP_5_Transform_and_ROI_drawing.m
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profile on
close all; clear all
addpath(genpath(pwd));
warning('off')
load('ANO_roi_edge');
load('Step_4_Angle_Search_Result');
load('Step_4to5_Cell_Detection_Result.mat') %% Load Cell detection From STEP4to5
STEP_0_Parameters;
img_name=Img_filename_list;
mkdir Image_Analysed
mkdir Image_Analysed_ROI_absent
elastixParams = {
strcat(pwd,'\Core_Functions\elastix_functions\warping_parameters_Affine.txt'),...
strcat(pwd,'\Core_Functions\elastix_functions\warping_parameters_BSpline.txt')}; %%% elastix
%% Prepartion : indices for both the anchor and non-anchor imgs
img_idx=anc_img_IDs;
ap_found=max_APpos_stage_final;
img_AP=[];
if length(img_idx) == 1
img_AP = ap_found;
else
for img_ID=1:length(img_idx)-1
img_AP=[img_AP, linspace(ap_found(img_ID),ap_found(img_ID+1),...
img_idx(img_ID+1)-img_idx(img_ID)+1)];
end
end
img_AP=round(unique(img_AP));
if Slice_AP_orPA==1
img_idx=min(img_idx):max(img_idx);
else
img_idx=max(img_idx):-1:min(img_idx);
end
%% LOAD ATLAS
if strcmp(Structure_stain,'DAPI') || strcmp(Structure_stain,'Nissl')
[VOL, metaVOL] = nrrdread('ara_nissl_25_2017.nrrd');
VOL=uint8(uint16(rot90(permute(VOL,[3 1 2]),3))/(2^8));
elseif strcmp(Structure_stain,'AutoF')
load('AutofluoresenceAtlas.mat');
VOL=rot90(permute(VOL,[3 1 2]),3);
else
error('Staining method not recognized');
end
yaw_found=yaw_stage5_max;
pitch_found=pitch_stage5_max;
tform_yaw=transform_matrix_0822( yaw_found,[0 1 0]);
tform_pitch=transform_matrix_0822(pitch_found,[1 0 0] );
tform_combined=mtimes(tform_yaw, tform_pitch);
tf_atlas= affine3d(tform_combined);
VOL_rot=imwarp(VOL,tf_atlas,'cubic');
ANO_rot=imwarp(ANO_roi_edge,tf_atlas,'nearest');
%% MAIN PART
parfor_progress(length(img_AP));
errorneous=false(1,length(img_AP));
img_essence(1:length(img_AP))=struct;
parfor img_ID=1:length(img_AP)
img_ID
if ~isempty(img_info(img_idx(img_ID)).slice_window)
img_essence(img_ID).img_AP_pos= img_AP(img_ID);
current_ap=img_AP(img_ID)-size(VOL,3)/2;
current_ap=round(size(VOL_rot,3)/2+current_ap*...
cosd(pitch_found)*cosd(yaw_found));
%%%%%%%%%%%%%%%%%%%%%%%% Atlas Slice Prepartion for Transformation %%%%%%%%%%%%%%%%%%%%
tform_general_resc_factor=1;
img_ref=uint8(squeeze(VOL_rot(:,:,current_ap)));
img_ref=imadjust(img_ref,stretchlim(img_ref,0),[0 1]);
img_ref=imresize(img_ref,tform_general_resc_factor);
img_ref=padarray(img_ref,round([3000 3000]/...
(ref_atlas_vox_res/tform_general_resc_factor)));
%%%%%%%%%%%%%%%%%%%%%%%%%%% Get Annotated Slice %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
img_ANO=uint8(squeeze(ANO_rot(:,:,current_ap)));
img_ANO=padarray(img_ANO,round([3000 3000]/(ref_atlas_vox_res)));
img_ANO_downscale=img_ANO;
img_ANO=imresize(img_ANO,(ref_atlas_vox_res/xy_pix),...
'method','nearest','Antialiasing',false);
%%%%%%%%%%%%%%%%%%%%%%%% Slice Preparation for Transformation %%%%%%%%%%%%%%%%%%%%%%%%%%
img_act=imread(img_name{img_idx(img_ID), Color_Channel_Structure});
try
img_act=rgb2gray(img_act);
end
img_act_pad=zeros(size(img_act));
img_act=img_act(img_info(img_idx(img_ID)).slice_window(1):...
img_info(img_idx(img_ID)).slice_window(2),...
img_info(img_idx(img_ID)).slice_window(3):...
img_info(img_idx(img_ID)).slice_window(4));
img_act_pad=img_act_pad(img_info(img_idx(img_ID)).slice_window(1):...
img_info(img_idx(img_ID)).slice_window(2),...
img_info(img_idx(img_ID)).slice_window(3):...
img_info(img_idx(img_ID)).slice_window(4));
img_act_pad(img_info(img_idx(img_ID)).bnd_pix_ind)=1;
img_act_pad=(imfill(img_act_pad));
img_act_pad=uint8(logical(img_act_pad));
img_act=img_act.*(img_act_pad);
img_act=padarray(img_act,round([3000 3000]/(xy_pix)));
img_act=imadjust(img_act,stretchlim(img_act,0.00),[0 1]);
img_act=img_act+( img_act-imgaussfilt(img_act,0.5*201,...
'FilterSize',[3 3]*603,'FilterDomain','frequency'))*5;
img_act=imresize(img_act,xy_pix/ref_atlas_vox_res*...
tform_general_resc_factor);
%%%%%%%%%%%%%%%%%%%%%%%%%%% Find Transformation Matrix %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
elastixDir_currImg = fullfile(pwd,...
strcat('\img_warping_log\img_ID_',num2str(img_ID))); %%% elastix
mkdir(elastixDir_currImg);
try
[matched_img,transform_params]=elastix(img_act, img_ref,elastixDir_currImg,elastixParams);
matched_img=uint8(matched_img);
end
if isempty(matched_img) || isempty(transform_params)
errorneous(img_ID)=true;
continue;
end
img_essence(img_ID).transform_params_downscaled=transform_params;
%%%%%%%%%%%%%%%%%%%%%%%%% Get DownScaled Img for 3D Rec. %%%%%%%%%%%%%%%%%%%%%%%
img_act_downscale = matched_img;
%%% Match size of images
whos_bigger=size(img_ANO_downscale)-size(img_act_downscale);
if whos_bigger(1)>=0; x_dim=size(img_ANO_downscale,1);
else; x_dim=size(img_act_downscale,1); end
if whos_bigger(2)>=0; y_dim=size(img_ANO_downscale,2);
else; y_dim=size(img_act_downscale,2); end
img_act_sizeMatch=[x_dim,y_dim]-size(img_act_downscale);
img_act_sizeMatch(img_act_sizeMatch<0)=0;
img_ANO_sizeMatch=[x_dim,y_dim]-size(img_ANO_downscale);
img_ANO_sizeMatch(img_ANO_sizeMatch<0)=0;
img_act_downscale=padarray(img_act_downscale,...
img_act_sizeMatch,'post');
img_essence(img_ID).transformed_img_downscaled=...
img_act_downscale;
%%%%%%%%%%%% Warp Images in Their Original Pix Resolution %%%%%%%%%%%%%%%%%%%%%%%
%%% modify transform parameters for warping IMAGES %%%
mov_scale_factor=(ref_atlas_vox_res/xy_pix);
transform_params_img_ori_scale=...
img_essence(img_ID).transform_params_downscaled
transform_params_img_ori_scale.TransformParameters{1, 1}.Size=...
fliplr(size(img_ANO)); %% elastix vs matlab...
transform_params_img_ori_scale.TransformParameters{1, 1}.TransformParameters(5:6) = ...
transform_params_img_ori_scale.TransformParameters{1, 1}.TransformParameters(5:6)*mov_scale_factor;
transform_params_img_ori_scale.TransformParameters{1, 1}.CenterOfRotationPoint = ...
round((fliplr(size(img_ref))/2)*mov_scale_factor);
transform_params_img_ori_scale.TransformParameters{1, 2}.Size=...
fliplr(size(img_ANO)); %% elastix vs matlab...
transform_params_img_ori_scale.TransformParameters{1, 2}.GridSpacing = ...
transform_params_img_ori_scale.TransformParameters{1, 2}.GridSpacing*mov_scale_factor;
transform_params_img_ori_scale.TransformParameters{1, 2}.GridOrigin = ...
transform_params_img_ori_scale.TransformParameters{1, 2}.GridOrigin*mov_scale_factor;
transform_params_img_ori_scale.TransformParameters{1, 2}.TransformParameters = ...
transform_params_img_ori_scale.TransformParameters{1, 2}.TransformParameters*mov_scale_factor;
%%% Recalculate transform parameters for warping CELL COORDINATES %%%
transform_params_cellPos_downscaled = ...
invertElastixTransform(elastixDir_currImg);
%%%NOTE: I know the line above seems redundant and costs you
%%%extra few minutes for recalculation, but transforming the
%%%cell coordinates using "transform_params_ori_scale" (used for
%%%image warping) kept giving me weird results. It also doesn't
%%%work the other way round (i.e.img warping with
%%%"transform_params_cellPos_downscaled")
img_essence(img_ID).transform_params_img_ori_scale= ...
transform_params_img_ori_scale;
img_essence(img_ID).transform_params_cellPos_downscaled= ...
transform_params_cellPos_downscaled;
%%% Load/Warp Images and Cell Pos in Original Resolution %%%
for color_ch_ID=1:length(Color_Channel_Interest)
cells_in_orig_img = ...
cell_detection_rs(img_ID).Color_Cells(color_ch_ID).cell_locations;
img_Color=(imread(img_name{img_idx(img_ID),...
Color_Channel_Interest(color_ch_ID)}));
try; img_Color=rgb2gray(img_Color); end
img_Color=img_Color(img_info(img_idx(img_ID)).slice_window(1):...
img_info(img_idx(img_ID)).slice_window(2),...
img_info(img_idx(img_ID)).slice_window(3):...
img_info(img_idx(img_ID)).slice_window(4));
img_Color=img_Color.*img_act_pad;
img_Color=padarray(img_Color,round([3000 3000]/(xy_pix)));
[img_warped_no_scale,~]=transformix(img_Color,...
transform_params_img_ori_scale);
img_warped_no_scale=uint8(img_warped_no_scale);
[cell_detected_all,~]=transformix(cells_in_orig_img/mov_scale_factor, ...
transform_params_cellPos_downscaled);
cell_detected_all=round(cell_detected_all.OutputPoint*...
mov_scale_factor); %%% Looks a bit weird, but works....
%%% Match size of annotation and warped images
whos_bigger=size(img_ANO)-size(img_warped_no_scale);
if whos_bigger(1)>=0; x_dim=size(img_ANO,1);
else; x_dim=size(img_warped_no_scale,1); end
if whos_bigger(2)>=0; y_dim=size(img_ANO,2);
else; y_dim=size(img_warped_no_scale,2); end
img_warped_sizeMatch=[x_dim,y_dim]-size(img_warped_no_scale);
img_warped_sizeMatch(img_warped_sizeMatch<0)=0;
img_ANO_sizeMatch=[x_dim,y_dim]-size(img_ANO);
img_ANO_sizeMatch(img_ANO_sizeMatch<0)=0;
img_ANO=padarray(img_ANO,img_ANO_sizeMatch,'post');
img_warped_no_scale=padarray(img_warped_no_scale,...
img_warped_sizeMatch,'post');
%%% nope nope nope don't use the below...
% [injection_site_pts] = injection_volume_pix( img_ch_thumbnail );
% img_essence(img_ID).injection.Color(color_ch_ID).valid_pts=injection_site_pts;
% img_essence(img_ID).injection.Color(color_ch_ID).image_thumbnail=img_ch_thumbnail;
% img_essence(img_ID).Color_image_downscaled(color_ch_ID).img=img_warped_no_scale;
%%%% for process monitoring (IMG) %%%%
monitoring_img=img_warped_no_scale;
monitoring_img_raw=monitoring_img;
ROI_map=cat(3,...
false(size(img_ANO)),logical(img_ANO),logical(img_ANO));
monitoring_img=imadjust(monitoring_img,...
stretchlim(monitoring_img,0),[0 1]);
monitoring_img=cat(3,...
monitoring_img,monitoring_img,monitoring_img);
monitoring_img(ROI_map)=255;
%%%% for process monitoring (CELL POS) %%%%
if ~isempty(cell_detected_all)
out_bnd_alpha = ref_boundarypad_0809_step5(...
img_warped_no_scale, xy_pix );
out_bnd=inShape(out_bnd_alpha,...
cell_detected_all(:,2),cell_detected_all(:,1));
cell_detected_all=cell_detected_all(~out_bnd,:);
end
if ~isempty(cell_detected_all)
cell_detected_all_pos_ind=sub2ind(size(img_warped_no_scale),...
cell_detected_all(:,2),cell_detected_all(:,1));
else
cell_detected_all_pos_ind=[];
end
img_essence(img_ID).Color_Cells(color_ch_ID).cell_locations=...
cell_detected_all;
%%%% for process monitoring (All TOGETHER) %%%%
image_analyzed_ROI=figure; %%% with ROI boundaries overlaid
imshow(monitoring_img,[]); hold on
title(strcat({'Image Name : '}, ...
img_name{img_idx(img_ID), Color_Channel_Interest(color_ch_ID)},...
{' - Ch No. '},num2str(color_ch_ID)),'Interpreter', 'none');
if ~isempty(cell_detected_all)
scatter(cell_detected_all(:,1),...
cell_detected_all(:,2),9,'r','filled')
end
image_analyzed=figure; %%% w/o ROI boundaries overlaid
imshow(monitoring_img_raw,[]); hold on
title(strcat({'Image Name : '}, ...
img_name{img_idx(img_ID), Color_Channel_Interest(color_ch_ID)},...
{' - Ch No. '},num2str(color_ch_ID)),'Interpreter', 'none');
if ~isempty(cell_detected_all)
scatter(cell_detected_all(:,1),...
cell_detected_all(:,2),9,'r','filled')
end
try
save_name=strcat('/Image_Analysed/',...
img_name{img_idx(img_ID), Color_Channel_Interest(color_ch_ID)},'.fig');
saveas( image_analyzed_ROI ,[pwd save_name]);
close(image_analyzed_ROI)
save_name=strcat('/Image_Analysed_ROI_absent/',...
img_name{img_idx(img_ID), Color_Channel_Interest(color_ch_ID)},'.fig');
saveas( image_analyzed,[pwd save_name]);
close(image_analyzed)
end
end
end
parfor_progress;
end
delete parfor_progress.txt
save('Step_5_Cell_Detection_Result','img_essence','-v7.3');
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