-
Notifications
You must be signed in to change notification settings - Fork 0
/
DanielS_ImageProcessingCommands.m
159 lines (125 loc) · 6.2 KB
/
DanielS_ImageProcessingCommands.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
% Code blocks are ordered newest to oldest
% Data.O.SegmentationParameters.DataSetName = '20170222_STRADa_SE_Eden_with_prctile_and_PxId';
% Data.O.General_Thresholds.Intensity_thr(1)=160;
% Ron LFS (With Cell Tracker)
DirName='\\carbon.research.sickkids.ca\rkafri\OPRETTA\Operetta Processed OutPutFiles\Dataset_20171103_RB_LFS__2017_11_03T17_30_39RESULTS';
FileName='SegPar_SegmentationParameters';
load([DirName '\' FileName])
Data.O.Collecting_X_Data='Collecting_prctile_data';
Data.O.Collecting_Histogram_Data='Collecting_Histogram_Data';
Data.O.Collecting_MoreRegionProps='Collecting_MoreRegionProps';
Data.O.Saving_Boundries='Saving_Boundries';
Data.O.Collecting_Morphological_Data='Collecting_Morphological_Data';
% Misc
Data.O.General_Thresholds.Intensity_thr(1)=160; % Looser threshold
Data.O.General_Thresholds.Label{1} = 'CellNucleus'; % Use DPC for both Cell and Nuclear channels, cause a nuclear channel is required by Ran's segmentation
% limit what is segmented
row = [5];
column = [2 7];
field = [19];
min_time = 193;
max_time = 193;
ImageIDs = Data.O.ImageIDs;
rows=ismember(ImageIDs.Row, row) & ismember(ImageIDs.Column, column) & ismember(ImageIDs.Field,field) & ImageIDs.Time <= max_time & ImageIDs.Time >= min_time;
Data.O.ImageIDs = Data.O.ImageIDs(rows,:);
[ResultTable]=O_SegmentCells_v6(Data);
% Eden STRADa (with prctile)
DirName='\\carbon.research.sickkids.ca\rkafri\OPRETTA\Operetta Processed OutPutFiles\Dataset_20170222_STRADa_SE_EdenRESULTS';
FileName='SegPar_SegmentationParameters';
load([DirName '\' FileName])
Data.O.Collecting_X_Data='Collecting_prctile_data';
Data.O.Collecting_Y_Data='Collecting_PerimPixelIdxList'; % now saving boundries
[ResultTable]=O_SegmentCells_v6(Data);
% Heather
DirName='\\carbon.research.sickkids.ca\rkafri\OPRETTA\Operetta Processed OutPutFiles\Dataset_20170322_TG_Fibroblast_movie_2RESULTS';
FileName='SegPar_SegmentationParameters2';
load([DirName '\' FileName])
Data.O.Collecting_X_Data='Collecting_Morphological_Data';
[ResultTable]=O_SegmentCells_v6(Data);
% Ceryl for tracking
DirName='\\carbon.research.sickkids.ca\rkafri\OPRETTA\Operetta Processed OutPutFiles\Dataset_20170811_CTSL_RPE1_movieRESULTS';
FileName='SegPar_SegmentationParameters';
load([DirName '\' FileName])
Data.O.Collecting_More_Data= { ...
'Collecting_MoreRegionProps', ...
% 'Saving_Boundries', ...
% 'Collecting_Morphological_Data', ...
% 'Collecting_Histogram_Data', ...
% 'Collecting_prctile_data', ...
};
% limit what is segmented
row = [5];
column = [3];
field = [2];
min_time = 1;
max_time = 247;
ImageIDs = Data.O.ImageIDs;
rows=ismember(ImageIDs.Row, row) & ismember(ImageIDs.Column, column) & ismember(ImageIDs.Field,field) & ImageIDs.Time <= max_time & ImageIDs.Time >= min_time;
Data.O.ImageIDs = Data.O.ImageIDs(rows,:);
[ResultTable]=O_SegmentCells_v6(Data);
% Camilla for tracking
DirName='\\carbon.research.sickkids.ca\rkafri\DanielS\Images\20180112_CG_DPC_ROS__2018-01-12T17_35_12-Measurement1_Field41';
FileName='SegPar_SegmentationParameters';
load([DirName '\' FileName])
Data.O.Collecting_More_Data= { ...
'Collecting_MoreRegionProps', ...
'Saving_Boundries', ...
'Collecting_Morphological_Data', ...
'Collecting_Histogram_Data', ...
'Collecting_prctile_data', ...
};
% limit what is segmented
row = [5];
column = [7];
field = [41];
min_time = 1;
max_time = 269;
ImageIDs = Data.O.ImageIDs;
rows=ismember(ImageIDs.Row, row) & ismember(ImageIDs.Column, column) & ismember(ImageIDs.Field,field) & ImageIDs.Time <= max_time & ImageIDs.Time >= min_time;
Data.O.ImageIDs = Data.O.ImageIDs(rows,:);
[ResultTable]=O_SegmentCells_v6(Data);
% Camilla Plates for TheWasserMAN
DirName='\\carbon.research.sickkids.ca\rkafri\OPRETTA\Operetta Processed OutPutFiles\Dataset_20171004_P5_pchk1_pS6RESULTS';
FileName='SegPar_SegmentationParameters';
load([DirName '\' FileName])
Data.O.Collecting_More_Data= { ...
'Collecting_MoreRegionProps', ...
'Saving_Boundries', ...
'Collecting_Morphological_Data', ...
'Collecting_Histogram_Data', ...
'Collecting_prctile_data', ...
};
[ResultTable2]=O_SegmentCells_v6(Data);
DirName='\\carbon.research.sickkids.ca\rkafri\OPRETTA\Operetta Processed OutPutFiles\Dataset_20171004_P2_p53_pS6RESULTS';
FileName='SegPar_SegmentationParameters';
load([DirName '\' FileName])
Data.O.Collecting_More_Data= { ...
'Collecting_MoreRegionProps', ...
'Saving_Boundries', ...
'Collecting_Morphological_Data', ...
'Collecting_Histogram_Data', ...
'Collecting_prctile_data', ...
};
[ResultTable3]=O_SegmentCells_v6(Data);
DirName='\\carbon.research.sickkids.ca\rkafri\OPRETTA\Operetta Processed OutPutFiles\Dataset_20171004_P2_p53_pH2AXRESULTS';
FileName='SegPar_SegmentationParameters';
load([DirName '\' FileName])
Data.O.Collecting_More_Data= { ...
'Collecting_MoreRegionProps', ...
'Saving_Boundries', ...
'Collecting_Morphological_Data', ...
'Collecting_Histogram_Data', ...
'Collecting_prctile_data', ...
};
[ResultTable4]=O_SegmentCells_v6(Data);
DirName='\\carbon.research.sickkids.ca\rkafri\OPRETTA\Operetta Processed OutPutFiles\Dataset_20171005_CG_PS6_PH2AXRESULTS';
FileName='SegPar_SegmentationParameters';
load([DirName '\' FileName])
Data.O.Collecting_More_Data= { ...
'Collecting_MoreRegionProps', ...
'Saving_Boundries', ...
'Collecting_Morphological_Data', ...
'Collecting_Histogram_Data', ...
'Collecting_prctile_data', ...
};
[ResultTable5]=O_SegmentCells_v6(Data);