-
Notifications
You must be signed in to change notification settings - Fork 5
/
microglia_whole_brain_segmentation.m
207 lines (169 loc) · 15.1 KB
/
microglia_whole_brain_segmentation.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
function [] = microglia_whole_brain_segmentation(varargin)
addpath('MORPHOLOGICAL_MASKING');
defaultDAPIpath='E:\50-plex\final\S1_R1C1.tif';
defaultHistonepath='E:\50-plex\final\S1_R2C2.tif';
defaultIBA1path='E:\50-plex\final\S1_R1C5.tif';
defaultOUTPUTdir='microglia_results';
defaultCLASSIFICATIONtable='E:\50-plex\classification_results\classification_table.csv';
defaultSEGMENTATIONmasks='data/merged_labelmask.txt';
p=inputParser;
addParameter(p,'DAPI_PATH',defaultDAPIpath,@ischar);
addParameter(p,'HISTONE_PATH',defaultHistonepath,@ischar);
addParameter(p,'IBA1_PATH',defaultIBA1path,@ischar);
addParameter(p,'OUTPUT_DIR',defaultOUTPUTdir,@ischar);
addParameter(p,'CLASSIFICATION_table_path',defaultCLASSIFICATIONtable,@ischar);
addParameter(p,'SEGMENTATION_masks',defaultSEGMENTATIONmasks,@ischar);
parse(p,varargin{:});
im_dapi_histone=imadd(imread(fullfile(p.Results.DAPI_PATH)),imread(fullfile(p.Results.HISTONE_PATH)));
im_iba1=imread(p.Results.IBA1_PATH);
%create output dir
if ~exist(p.Results.OUTPUT_DIR,'dir')
mkdir(p.Results.OUTPUT_DIR)
end
%load boundingboxes
x0=0;y0=0;
W=size(im_dapi_histone,2);
H=size(im_dapi_histone,1);
bbxs=get_bbxs_csv(p.Results.CLASSIFICATION_table_path,W,H,x0,y0);
xc=bbxs.centroid_x;
yc=bbxs.centroid_y;
IDs=bbxs.ID;
%load segmentation masks
seg_masks=readtable(p.Results.SEGMENTATION_masks);
seg_masks_array=table2array(seg_masks);
seg_masks_props=regionprops(seg_masks_array,'Centroid','Image','BoundingBox');
seg_masks_c=vertcat(seg_masks_props.Centroid);
half_w_p=100;
w_n=50;
w_s=100;
w_p=200;
% all_cell_type=zeros(size(im_dapi_histone,1),size(im_dapi_histone,2),3);
%
% all_micro_nucleus=zeros(size(im_dapi_histone));
% all_micro_soma=zeros(size(im_dapi_histone));
% all_micro_processes=zeros(size(im_dapi_histone));
% all_micro_cytoplasm=zeros(size(im_dapi_histone));
% all_micro_membrane=zeros(size(im_dapi_histone));
% all_micro_whole_cell=zeros(size(im_dapi_histone));
microglia_results = struct('index',{},'cell_type',{},'nucleus_x1',{},'nucleus_x2',{},'nucleus_y1',{},'nucleus_y2',{},'nucleus_img',{},...
'x_c',{},'y_c',{},'soma_x1',{},'soma_x2',{},'soma_y1',{},'soma_y2',{},'soma_img',{},...
'cell_x1',{},'cell_x2',{},'cell_y1',{},'cell_y2',{},'processes_img',{},'membrane_img',{},'cytoplasm_img',{},'cell_img',{});
cnt=1;
for i=1: length(xc)
[row,dist]=find_closest_points_index_cnst(seg_masks_c(:,1),seg_masks_c(:,2),xc(i),yc(i)); % find corresponding masks for the boundind box
iba1_val=bbxs.Iba1(i);
if iba1_val==1 && dist<50
disp(strcat('Iteration: ',int2str(IDs(i))));
BB=seg_masks_props(row).BoundingBox;
x1=ceil(BB(1));
y1=ceil(BB(2));
x2=x1+BB(3)-1;
y2=y1+BB(4)-1;
x_c=seg_masks_c(row,1);
y_c=seg_masks_c(row,2);
half_wd=round((x2-x1)/2);
half_ht=round((y2-y1)/2);
nucleus_mask1=zeros(w_p+1,w_p+1);
nucleus_mask1(1+half_w_p-half_ht:1+half_w_p+y2-y1-half_ht,1+half_w_p-half_wd:1+half_w_p+x2-x1-half_wd)=seg_masks_props(row).Image;
microglia_results(cnt).index=IDs(i);
microglia_results(cnt).cell_type=1; %Astrocyte, S100 is astrocyte pan-specific
[soma_mask, processes, cytoplasm, membrane, whole_cell] = microglia_segmentation_v3(im_iba1,nucleus_mask1,x_c,y_c,w_n,w_s,w_p);
microglia_results(cnt).nucleus_img = uint8(nucleus_mask1);
microglia_results(cnt).nucleus_x1 = x1 - x_c +half_w_p;
microglia_results(cnt).nucleus_x2 = x2 - x_c +half_w_p;
microglia_results(cnt).nucleus_y1 = y1 - y_c +half_w_p;
microglia_results(cnt).nucleus_y2 = y2 - y_c +half_w_p;
microglia_results(cnt).x_c=x_c;
microglia_results(cnt).y_c=y_c;
soma_props=regionprops(bwconncomp(soma_mask+nucleus_mask1,4)); %added coz soma mask might be split too
soma_cs=vertcat(soma_props.Centroid);
soma_cx=soma_cs(:,1);
soma_cy=soma_cs(:,2);
soma_idx = find_closest_points_index_cnst(soma_cx,soma_cy,size(soma_mask,1)/2,size(soma_mask,2)/2);
%added coz soma mask might be split too
soma_BB=soma_props(soma_idx).BoundingBox;
microglia_results(cnt).soma_x1=ceil(soma_BB(1));
microglia_results(cnt).soma_x2=soma_BB(3)-1+ceil(soma_BB(1));
microglia_results(cnt).soma_y1=ceil(soma_BB(2));
microglia_results(cnt).soma_y2=soma_BB(4)-1+ceil(soma_BB(2));
microglia_results(cnt).soma_img=uint8(soma_mask);
whole_cell_props=regionprops(bwconncomp(whole_cell,4));
whole_cell_cs=vertcat(whole_cell_props.Centroid);
whole_cell_cx=whole_cell_cs(:,1);
whole_cell_cy=whole_cell_cs(:,2);
whole_cell_idx = find_closest_points_index_cnst(whole_cell_cx,whole_cell_cy,w_p/2,w_p/2);
whole_cell_BB=whole_cell_props(whole_cell_idx).BoundingBox;
microglia_results(cnt).cell_x1=ceil(whole_cell_BB(1));
microglia_results(cnt).cell_x2=ceil(whole_cell_BB(1))+whole_cell_BB(3)-1;
microglia_results(cnt).cell_y1=ceil(whole_cell_BB(2));
microglia_results(cnt).cell_y2=ceil(whole_cell_BB(2))+whole_cell_BB(4)-1;
microglia_results(cnt).cell_img=uint8(whole_cell);
microglia_results(cnt).processes_img=uint8(processes);
microglia_results(cnt).cytoplasm_img=uint8(cytoplasm);
microglia_results(cnt).membrane_img=uint8(membrane);
% all_cell_type(y_c-2:y_c+2,x_c-2:x_c+2,1)=0;
% all_cell_type(y_c-2:y_c+2,x_c-2:x_c+2,2)=255;
% all_cell_type(y_c-2:y_c+2,x_c-2:x_c+2,3)=0;
%
% all_micro_nucleus(microglia_results(cnt).y1:microglia_results(cnt).y2,microglia_results(cnt).x1:microglia_results(cnt).x2)=microglia_results(cnt).nucleus_img+all_micro_nucleus(microglia_results(cnt).y1:microglia_results(cnt).y2,microglia_results(cnt).x1:microglia_results(cnt).x2);
% all_micro_soma(microglia_results(cnt).soma_y1:microglia_results(cnt).soma_y2,microglia_results(cnt).soma_x1:microglia_results(cnt).soma_x2)=microglia_results(cnt).soma_img+all_micro_soma(microglia_results(cnt).soma_y1:microglia_results(cnt).soma_y2,microglia_results(cnt).soma_x1:microglia_results(cnt).soma_x2);
% all_micro_whole_cell(microglia_results(cnt).cell_y1:microglia_results(cnt).cell_y2,microglia_results(cnt).cell_x1:microglia_results(cnt).cell_x2)=microglia_results(cnt).cell_img+all_micro_whole_cell(microglia_results(cnt).cell_y1:microglia_results(cnt).cell_y2,microglia_results(cnt).cell_x1:microglia_results(cnt).cell_x2);
% all_micro_processes(microglia_results(cnt).cell_y1:microglia_results(cnt).cell_y2,microglia_results(cnt).cell_x1:microglia_results(cnt).cell_x2)=microglia_results(cnt).processes_img+all_micro_processes(microglia_results(cnt).cell_y1:microglia_results(cnt).cell_y2,microglia_results(cnt).cell_x1:microglia_results(cnt).cell_x2);
% all_micro_cytoplasm(microglia_results(cnt).cell_y1:microglia_results(cnt).cell_y2,microglia_results(cnt).cell_x1:microglia_results(cnt).cell_x2)=microglia_results(cnt).cytoplasm_img+all_micro_cytoplasm(microglia_results(cnt).cell_y1:microglia_results(cnt).cell_y2,microglia_results(cnt).cell_x1:microglia_results(cnt).cell_x2);
% all_micro_membrane(microglia_results(cnt).cell_y1:microglia_results(cnt).cell_y2,microglia_results(cnt).cell_x1:microglia_results(cnt).cell_x2)=microglia_results(cnt).membrane_img+all_micro_membrane(microglia_results(cnt).cell_y1:microglia_results(cnt).cell_y2,microglia_results(cnt).cell_x1:microglia_results(cnt).cell_x2);
cnt=cnt+1;
end
end
% imwrite(all_cell_type,fullfile(p.Results.OUTPUT_DIR,'micro_cell_type.tif'));
% imwrite(im2uint8(all_micro_nucleus),fullfile(p.Results.OUTPUT_DIR,'micro_nucleus_mask.tif'));
% imwrite(im2uint8(all_micro_soma),fullfile(p.Results.OUTPUT_DIR,'micro_soma_mask.tif'));
% imwrite(im2uint8(all_micro_processes),fullfile(p.Results.OUTPUT_DIR,'micro_processes_mask.tif'));
% imwrite(im2uint8(all_micro_membrane),fullfile(p.Results.OUTPUT_DIR,'micro_membrane_mask.tif'));
% imwrite(im2uint8(all_micro_cytoplasm),fullfile(p.Results.OUTPUT_DIR,'micro_cytoplasm_mask.tif'));
% imwrite(im2uint8(all_micro_whole_cell),fullfile(p.Results.OUTPUT_DIR,'micro_whole_cell_mask.tif'));
% save(fullfile(p.Results.OUTPUT_DIR,'micro_reconstruction_info.mat'),'microglia_results');
h5create(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/index', size(microglia_results));%.index));
h5create(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/cell_type', size(microglia_results));%.cell_type));
h5create(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/nucleus_x1', size(microglia_results));%.nuclues_x1));
h5create(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/nucleus_x2', size(microglia_results));%.nucleus_x2));
h5create(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/nucleus_y1', size(microglia_results));%.nucleus_y1));
h5create(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/nucleus_y2', size(microglia_results));%.nucleus_y2));
h5create(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/nucleus_img', [w_p+1,w_p+1,size(microglia_results,1),size(microglia_results,2)]);%.nucleus_img));
h5create(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/x_c', size(microglia_results));%.x_c));
h5create(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/y_c', size(microglia_results));%.y_c));
h5create(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/soma_x1', size(microglia_results));%.soma_x1));
h5create(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/soma_x2', size(microglia_results));%.soma_x2));
h5create(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/soma_y1', size(microglia_results));%.soma_y1));
h5create(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/soma_y2', size(microglia_results));%.soma_y2));
h5create(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/soma_img',[w_p+1,w_p+1,size(microglia_results,1),size(microglia_results,2)]);%.soma_img));
h5create(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/cell_x1', size(microglia_results));%.cell_x1));
h5create(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/cell_x2', size(microglia_results));%.cell_x2));
h5create(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/cell_y1', size(microglia_results));%.cell_y1));
h5create(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/cell_y2', size(microglia_results));%.cell_y2));
h5create(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/processes_img', [w_p+1,w_p+1,size(microglia_results,1),size(microglia_results,2)]);%.processes_img));
h5create(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/membrane_img', [w_p+1,w_p+1,size(microglia_results,1),size(microglia_results,2)]);%.membrane_img));
h5create(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/cytoplasm_img', [w_p+1,w_p+1,size(microglia_results,1),size(microglia_results,2)]);%.cytoplasm_img));
h5create(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/cell_img', [w_p+1,w_p+1,size(microglia_results,1),size(microglia_results,2)]);%.cell_img));
h5write(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/index', cell2mat({microglia_results.index}));
h5write(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/cell_type', cell2mat({microglia_results.cell_type}));
h5write(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/nucleus_x1', cell2mat({microglia_results.nucleus_x1}));
h5write(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/nucleus_x2', cell2mat({microglia_results.nucleus_x2}));
h5write(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/nucleus_y1', cell2mat({microglia_results.nucleus_y1}));
h5write(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/nucleus_y2', cell2mat({microglia_results.nucleus_y2}));
h5write(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/nucleus_img', reshape(cell2mat({microglia_results.nucleus_img}),[w_p+1,w_p+1,size(microglia_results,1),size(microglia_results,2)]));
h5write(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/x_c', cell2mat({microglia_results.x_c}));
h5write(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/y_c', cell2mat({microglia_results.y_c}));
h5write(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/soma_x1', cell2mat({microglia_results.soma_x1}));
h5write(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/soma_x2', cell2mat({microglia_results.soma_x2}));
h5write(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/soma_y1', cell2mat({microglia_results.soma_y1}));
h5write(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/soma_y2', cell2mat({microglia_results.soma_y2}));
h5write(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/soma_img', reshape(cell2mat({microglia_results.soma_img}),[w_p+1,w_p+1,size(microglia_results,1),size(microglia_results,2)]));
h5write(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/cell_x1', cell2mat({microglia_results.cell_x1}));
h5write(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/cell_x2', cell2mat({microglia_results.cell_x2}));
h5write(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/cell_y1', cell2mat({microglia_results.cell_y1}));
h5write(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/cell_y2', cell2mat({microglia_results.cell_y2}));
h5write(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/processes_img', reshape(cell2mat({microglia_results.processes_img}),[w_p+1,w_p+1,size(microglia_results,1),size(microglia_results,2)]));
h5write(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/membrane_img', reshape(cell2mat({microglia_results.membrane_img}),[w_p+1,w_p+1,size(microglia_results,1),size(microglia_results,2)]));
h5write(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/cytoplasm_img', reshape(cell2mat({microglia_results.cytoplasm_img}),[w_p+1,w_p+1,size(microglia_results,1),size(microglia_results,2)]));
h5write(fullfile(p.Results.OUTPUT_DIR,'microglia_reconstruction_results.h5'),'/cell_img', reshape(cell2mat({microglia_results.cell_img}),[w_p+1,w_p+1,size(microglia_results,1),size(microglia_results,2)]));
end