Commit 1900f34

CellProfiler Pipeline: http://www.cellprofiler.org

Version:5

DateRevision:413

GitHash:

ModuleCount:6

HasImagePlaneDetails:False

Images:[module_num:1|svn_version:'Unknown'|variable_revision_number:2|show_window:False|notes:['To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]

:

Filter images?:Images only

Select the rule criteria:and (extension does isimage) (directory doesnot containregexp "[\\\\/]\\.")

Metadata:[module_num:2|svn_version:'Unknown'|variable_revision_number:6|show_window:False|notes:['The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]

Extract metadata?:Yes

Metadata data type:Text

Metadata types:{}

Extraction method count:1

Metadata extraction method:Extract from image file headers

Metadata source:File name

Regular expression to extract from file name:^(?P<Plate>.*)_(?P<Well>[A-P][0-9]{2})_s(?P<Site>[0-9])_w(?P<ChannelNumber>[0-9])

Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$

Extract metadata from:All images

Select the filtering criteria:and (file does contain "")

Metadata file location:Elsewhere...|

Match file and image metadata:[]

Use case insensitive matching?:No

Metadata file name:None

Does cached metadata exist?:Yes

NamesAndTypes:[module_num:3|svn_version:'Unknown'|variable_revision_number:8|show_window:False|notes:['The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]

Assign a name to:All images

Select the image type:Grayscale image

Name to assign these images:image

Match metadata:[{'Cytoplasm': 'FileLocation', 'DNA': 'FileLocation'}]

Image set matching method:Order

Set intensity range from:Image metadata

Assignments count:2

Single images count:0

Maximum intensity:255.0

Process as 3D?:No

Relative pixel spacing in X:1.0

Relative pixel spacing in Y:1.0

Relative pixel spacing in Z:1.0

Select the rule criteria:and (metadata does C "0")

Name to assign these images:DNA

Name to assign these objects:Cell

Select the image type:Grayscale image

Set intensity range from:Image metadata

Maximum intensity:255.0

Select the rule criteria:and (metadata does C "1")

Name to assign these images:Cytoplasm

Name to assign these objects:Cell

Select the image type:Grayscale image

Set intensity range from:Image metadata

Maximum intensity:255.0

Groups:[module_num:4|svn_version:'Unknown'|variable_revision_number:2|show_window:False|notes:['The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]

Do you want to group your images?:Yes

grouping metadata count:2

Metadata category:C

Metadata category:FileLocation

MakeProjection:[module_num:5|svn_version:'Unknown'|variable_revision_number:2|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]

Select the input image:image

Type of projection:Maximum

Name the output image:ProjectedImage

Frequency:6.0

SaveImages:[module_num:6|svn_version:'Unknown'|variable_revision_number:15|show_window:False|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]

Select the type of image to save:Image

Select the image to save:ProjectedImage

Select method for constructing file names:From image filename

Select image name for file prefix:image

Enter single file name:OrigBlue

Number of digits:4

Append a suffix to the image file name?:Yes

Text to append to the image name:_\g<C>

Saved file format:tiff

Output file location:Default Output Folder|

Image bit depth:8-bit integer

Overwrite existing files without warning?:No

When to save:Last cycle

Record the file and path information to the saved image?:No

Create subfolders in the output folder?:No

Base image folder:Elsewhere...|

How to save the series:T (Time)