-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy path110803TemplatePipelineCountInfectedCells3Chan.cp
167 lines (160 loc) · 8.27 KB
/
110803TemplatePipelineCountInfectedCells3Chan.cp
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
CellProfiler Pipeline: http://www.cellprofiler.org
Version:1
SVNRevision:11000
LoadImages:[module_num:1|svn_version:\'10951\'|variable_revision_number:11|show_window:False|notes:\x5B\x5D]
File type to be loaded:individual images
File selection method:Text-Regular expressions
Number of images in each group?:3
Type the text that the excluded images have in common:Do not use
Analyze all subfolders within the selected folder?:All
Input image file location:Default Input Folder\x7CNone
Check image sets for missing or duplicate files?:Yes
Group images by metadata?:Yes
Exclude certain files?:No
Specify metadata fields to group by:Well
Select subfolders to analyze:
Image count:3
Text that these images have in common (case-sensitive):\\w*w1.TIF
Position of this image in each group:1
Extract metadata from where?:File name
Regular expression that finds metadata in the file name:^(?P<Plate>.*)_(?P<Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P<Site>\x5B0-9\x5D*)
Type the regular expression that finds metadata in the subfolder path:.*\x5B\\\\/\x5D(?P<Date>.*)\x5B\\\\/\x5D(?P<Run>.*)$
Channel count:1
Group the movie frames?:No
Grouping method:Interleaved
Number of channels per group:2
Load the input as images or objects?:Images
Name this loaded image:Nuclei
Name this loaded object:Nuclei
Retain outlines of loaded objects?:No
Name the outline image:NucleiOutlines
Channel number:1
Rescale intensities?:Yes
Text that these images have in common (case-sensitive):\\w*w2.TIF
Position of this image in each group:2
Extract metadata from where?:File name
Regular expression that finds metadata in the file name:^(?P<Plate>.*)_(?P<Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P<Site>\x5B0-9\x5D*)
Type the regular expression that finds metadata in the subfolder path:.*\x5B\\\\/\x5D(?P<Date>.*)\x5B\\\\/\x5D(?P<Run>.*)$
Channel count:1
Group the movie frames?:No
Grouping method:Interleaved
Number of channels per group:2
Load the input as images or objects?:Images
Name this loaded image:VirusSignal
Name this loaded object:Nuclei
Retain outlines of loaded objects?:No
Name the outline image:NucleiOutlines
Channel number:1
Rescale intensities?:Yes
Text that these images have in common (case-sensitive):\\w*w3.TIF
Position of this image in each group:3
Extract metadata from where?:File name
Regular expression that finds metadata in the file name:^(?P<Plate>.*)_(?P<Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P<Site>\x5B0-9\x5D)
Type the regular expression that finds metadata in the subfolder path:.*\x5B\\\\/\x5D(?P<Date>.*)\x5B\\\\/\x5D(?P<Run>.*)$
Channel count:1
Group the movie frames?:No
Grouping method:Interleaved
Number of channels per group:3
Load the input as images or objects?:Images
Name this loaded image:RedChan
Name this loaded object:Nuclei
Retain outlines of loaded objects?:No
Name the outline image:LoadedImageOutlines
Channel number:1
Rescale intensities?:Yes
IdentifyPrimaryObjects:[module_num:2|svn_version:\'10826\'|variable_revision_number:8|show_window:False|notes:\x5B\x5D]
Select the input image:Nuclei
Name the primary objects to be identified:DetectedNuclei
Typical diameter of objects, in pixel units (Min,Max):10,45
Discard objects outside the diameter range?:Yes
Try to merge too small objects with nearby larger objects?:No
Discard objects touching the border of the image?:Yes
Select the thresholding method:Otsu Global
Threshold correction factor:1
Lower and upper bounds on threshold:0.000000,1.000000
Approximate fraction of image covered by objects?:0.01
Method to distinguish clumped objects:Intensity
Method to draw dividing lines between clumped objects:Intensity
Size of smoothing filter:10
Suppress local maxima that are closer than this minimum allowed distance:7
Speed up by using lower-resolution image to find local maxima?:Yes
Name the outline image:PrimaryOutlines
Fill holes in identified objects?:No
Automatically calculate size of smoothing filter?:Yes
Automatically calculate minimum allowed distance between local maxima?:Yes
Manual threshold:0.0
Select binary image:None
Retain outlines of the identified objects?:No
Automatically calculate the threshold using the Otsu method?:Yes
Enter Laplacian of Gaussian threshold:0.5
Two-class or three-class thresholding?:Two classes
Minimize the weighted variance or the entropy?:Weighted variance
Assign pixels in the middle intensity class to the foreground or the background?:Foreground
Automatically calculate the size of objects for the Laplacian of Gaussian filter?:Yes
Enter LoG filter diameter:5
Handling of objects if excessive number of objects identified:Continue
Maximum number of objects:500
Select the measurement to threshold with:None
IdentifySecondaryObjects:[module_num:3|svn_version:\'10826\'|variable_revision_number:7|show_window:False|notes:\x5B\x5D]
Select the input objects:DetectedNuclei
Name the objects to be identified:Cells
Select the method to identify the secondary objects:Distance - N
Select the input image:VirusSignal
Select the thresholding method:Otsu Global
Threshold correction factor:1
Lower and upper bounds on threshold:0.000000,1.000000
Approximate fraction of image covered by objects?:0.01
Number of pixels by which to expand the primary objects:5
Regularization factor:0.05
Name the outline image:SecondaryOutlines
Manual threshold:0.0
Select binary image:None
Retain outlines of the identified secondary objects?:No
Two-class or three-class thresholding?:Two classes
Minimize the weighted variance or the entropy?:Weighted variance
Assign pixels in the middle intensity class to the foreground or the background?:Foreground
Discard secondary objects that touch the edge of the image?:No
Discard the associated primary objects?:No
Name the new primary objects:FilteredNuclei
Retain outlines of the new primary objects?:No
Name the new primary object outlines:FilteredNucleiOutlines
Select the measurement to threshold with:None
Fill holes in identified objects?:No
IdentifyTertiaryObjects:[module_num:4|svn_version:\'10300\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D]
Select the larger identified objects:Cells
Select the smaller identified objects:DetectedNuclei
Name the tertiary objects to be identified:Cytoplasm
Name the outline image:CytoplasmOutlines
Retain outlines of the tertiary objects?:No
MeasureObjectIntensity:[module_num:5|svn_version:\'10816\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D]
Hidden:1
Select an image to measure:VirusSignal
Select objects to measure:Cells
Select objects to measure:DetectedNuclei
Select objects to measure:Cytoplasm
MeasureObjectIntensity:[module_num:6|svn_version:\'10816\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D]
Hidden:1
Select an image to measure:RedChan
Select objects to measure:Cells
Select objects to measure:DetectedNuclei
Select objects to measure:Cytoplasm
ExportToSpreadsheet:[module_num:7|svn_version:\'10880\'|variable_revision_number:7|show_window:False|notes:\x5B\x5D]
Select or enter the column delimiter:Comma (",")
Prepend the output file name to the data file names?:Yes
Add image metadata columns to your object data file?:Yes
Limit output to a size that is allowed in Excel?:No
Select the columns of measurements to export?:No
Calculate the per-image mean values for object measurements?:No
Calculate the per-image median values for object measurements?:No
Calculate the per-image standard deviation values for object measurements?:No
Output file location:Default Output Folder\x7CNone
Create a GenePattern GCT file?:No
Select source of sample row name:Metadata
Select the image to use as the identifier:None
Select the metadata to use as the identifier:None
Export all measurements, using default file names?:Yes
Press button to select measurements to export:
Data to export:Do not use
Combine these object measurements with those of the previous object?:No
File name:DATA.csv
Use the object name for the file name?:Yes