Saved Pipeline, in file Astrazeneca_FinalPIPE.txt, Saved on 24-Oct-2011

SVN version number: 9405
Pixel Size: 1

Pipeline:
	LoadImages
	FileNameMetadata
	LoadSingleImage
	LoadText
	LoadText
	CorrectIllumination_Apply
	CorrectIllumination_Apply
	CorrectIllumination_Apply
	IdentifyPrimAutomatic
	IdentifySecondary
	IdentifyTertiarySubregion
	MeasureObjectAreaShape
	MeasureObjectIntensity
	MeasureObjectIntensity
	MeasureObjectIntensity
	MeasureObjectNeighbors
	MeasureObjectNeighbors
	MeasureObjectNeighbors
	MeasureObjectNeighbors
	MeasureTexture
	MeasureTexture
	MeasureTexture
	MeasureTexture
	MeasureTexture
	MeasureTexture
	SaveImages
	ExportToDatabase
	CreateBatchFiles

Module #1: LoadImages revision - 5
     How do you want to load these files?    Text-Exact match
     Type the text that one type of image has in common (for TEXT options), or their position in each group (for ORDER option):    _w1
     What do you want to call these images within CellProfiler?    DAPI
     Type the text that one type of image has in common (for TEXT options), or their position in each group (for ORDER option). Type "Do not use" to ignore:    _w2
     What do you want to call these images within CellProfiler? (Type "Do not use" to ignore)    Actin
     Type the text that one type of image has in common (for TEXT options), or their position in each group (for ORDER option):    _w3
     What do you want to call these images within CellProfiler?    Tubulin
     Type the text that one type of image has in common (for TEXT options), or their position in each group (for ORDER option):    Do not use
     What do you want to call these images within CellProfiler?    Do not use
     If using ORDER, how many images are there in each group (i.e. each field of view)?    3
     If you want to exclude files, type the text that the excluded images have in common (for TEXT options). Type "Do not use" to ignore.    Do not use
     What type of files are you loading?    individual images
     Analyze all subfolders within the selected folder?    Yes
     Enter the path name to the folder where the images to be loaded are located. Type period (.) for default image folder or ampersand (&) for default output folder.    .
     If the images you are loading are binary (black/white only), in what format do you want to store them?    grayscale
     If Yes to "Analyze all subfolders", do you want to select the subfolders to process?    No
     Do you want to check image sets for missing or duplicate files? Tokens must be defined for the unique parts of the string. (REGULAR EXPRESSIONS ONLY)    No
     Note - If the movies contain more than just one image type (e.g., brightfield, fluorescent, field-of-view), add the GroupMovieFrames module.      

Module #2: FileNameMetadata revision - 4
     What did you call the image?    DAPI
     For the filename, enter the regular expression to use to capture the fields. Type "Do not use" to ignore.    Do not use
     For the pathname, enter the regular expression to use to capture the fields. Separate each directory-specific field using vertical lines (i.e, | ). Type "Do not use" to ignore.    /Week1/(?<Plate>.+)
     If you want to group the images according to a set of tokens, enter the fields here, separated by commas. Type "Do not use" to ignore.    Do not use

Module #3: LoadSingleImage revision - 4
     This module loads one image for *all* cycles that will be processed. Typically, however, a different module (LoadImages) is used to load new sets of images during each cycle of processing.    n/a
     Enter the path name to the folder where the images to be loaded are located.  Type period (.) for the default image folder, or type ampersand (&) for the default output folder.    .
     What image file do you want to load? Include the extension, like .tif    (?<Plate>)DAPI.mat
     What do you want to call that image?    DAPIillum
     What image file do you want to load? Include the extension, like .tif    (?<Plate>)Actin.mat
     What do you want to call that image?    ActinIllum
     What image file do you want to load? Include the extension, like .tif    (?<Plate>)Tubulin.mat
     What do you want to call that image?    TubIllum
     What image file do you want to load? Include the extension, like .tif    Do not use
     What do you want to call that image?    Do not use

Module #4: LoadText revision - 2
     What is the file containing the text that you want to load?    Week1platemap.txt
     What would you like to call the loaded text?    platemap
     Enter the path name to the folder where the text file to be loaded is located.  Type period (.) for the default image folder, or ampersand (&) for the default output folder.    .

Module #5: LoadText revision - 2
     What is the file containing the text that you want to load?    week1_cpds_FINAL.txt
     What would you like to call the loaded text?    Compounds
     Enter the path name to the folder where the text file to be loaded is located.  Type period (.) for the default image folder, or ampersand (&) for the default output folder.    .

Module #6: CorrectIllumination_Apply revision - 3
     What did you call the image to be corrected?    DAPI
     What do you want to call the corrected image?    CorrDAPI
     What did you call the illumination correction function image to be used to carry out the correction (produced by another module or loaded as a .mat format image using Load Single Image)?    DAPIillum
     How do you want to apply the illumination correction function?    Divide
     If you chose division, Choose rescaling method.    Stretch 0 to 1

Module #7: CorrectIllumination_Apply revision - 3
     What did you call the image to be corrected?    Actin
     What do you want to call the corrected image?    CorrActin
     What did you call the illumination correction function image to be used to carry out the correction (produced by another module or loaded as a .mat format image using Load Single Image)?    ActinIllum
     How do you want to apply the illumination correction function?    Divide
     If you chose division, Choose rescaling method.    Stretch 0 to 1

Module #8: CorrectIllumination_Apply revision - 3
     What did you call the image to be corrected?    Tubulin
     What do you want to call the corrected image?    CorrTub
     What did you call the illumination correction function image to be used to carry out the correction (produced by another module or loaded as a .mat format image using Load Single Image)?    TubIllum
     How do you want to apply the illumination correction function?    Divide
     If you chose division, Choose rescaling method.    Stretch 0 to 1

Module #9: IdentifyPrimAutomatic revision - 12
     What did you call the images you want to process?    CorrDAPI
     What do you want to call the objects identified by this module?    Nuclei
     Typical diameter of objects, in pixel units (Min,Max):    6,115
     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 an automatic thresholding method or enter an absolute threshold in the range [0,1].  To choose a binary image, select "Other" and type its name.  Choosing 'All' will use the Otsu Global method to calculate a single threshold for the entire image group. The other methods calculate a threshold for each image individually. "Set interactively" will allow you to manually adjust the threshold during the first cycle to determine what will work well.    Otsu Global
     Threshold correction factor    1
     Lower and upper bounds on threshold, in the range [0,1]    0,1
     For MoG thresholding, what is the approximate fraction of image covered by objects?    0.01
     Method to distinguish clumped objects (see help for details):    Shape
      Method to draw dividing lines between clumped objects (see help for details):    Intensity
     Size of smoothing filter, in pixel units (if you are distinguishing between clumped objects). Enter 0 for low resolution images with small objects (~< 5 pixel diameter) to prevent any image smoothing.    10
     Suppress local maxima within this distance, (a positive integer, in pixel units) (if you are distinguishing between clumped objects)    Automatic
     Speed up by using lower-resolution image to find local maxima?  (if you are distinguishing between clumped objects)    Yes
     Enter the following information, separated by commas, if you would like to use the Laplacian of Gaussian method for identifying objects instead of using the above settings: Size of neighborhood(height,width),Sigma,Minimum Area,Size for Wiener Filter(height,width),Threshold    Do not use
     What do you want to call the outlines of the identified objects (optional)?    Do not use
     Do you want to fill holes in identified objects?    Yes
     Do you want to run in test mode where each method for distinguishing clumped objects is compared?    No

Module #10: IdentifySecondary revision - 3
     What did you call the primary objects you want to create secondary objects around?    Nuclei
     What do you want to call the objects identified by this module?    Cells
     Select the method to identify the secondary objects (Distance - B uses background; Distance - N does not):    Propagation
     What did you call the images to be used to find the edges of the secondary objects? For DISTANCE - N, this will not affect object identification, only the final display.    CorrActin
     Select an automatic thresholding method or enter an absolute threshold in the range [0,1]. To choose a binary image, select "Other" and type its name.  Choosing 'All' will use the Otsu Global method to calculate a single threshold for the entire image group. The other methods calculate a threshold for each image individually. Set interactively will allow you to manually adjust the threshold during the first cycle to determine what will work well.    Otsu Global
     Threshold correction factor    1
     Lower and upper bounds on threshold, in the range [0,1]    0,1
     For MoG thresholding, what is the approximate fraction of image covered by objects?    0.01
     For DISTANCE, enter the number of pixels by which to expand the primary objects [Positive integer]    10
     For PROPAGATION, enter the regularization factor (0 to infinity). Larger=distance,0=intensity    0.05
     What do you want to call the outlines of the identified objects (optional)?    CellOutline
     Do you want to run in test mode where each method for identifying secondary objects is compared?    No

Module #11: IdentifyTertiarySubregion revision - 1
     What did you call the larger identified objects?    Cells
     What did you call the smaller identified objects?    Nuclei
     What do you want to call the new subregions?    Cytoplasm
     What do you want to call the outlines of the identified objects (optional)?    Do not use

Module #12: MeasureObjectAreaShape revision - 3
     What did you call the objects that you want to measure?    Nuclei
        Cells
        Cytoplasm
        Do not use
        Do not use
        Do not use
        Do not use
     Would you like to calculate the Zernike features for each object (with lots of objects, this can be very slow)?    Yes

Module #13: MeasureObjectIntensity revision - 2
     What did you call the greyscale images you want to measure?    CorrDAPI
     What did you call the objects that you want to measure?    Nuclei
        Do not use
        Do not use
        Do not use
        Do not use
        Do not use

Module #14: MeasureObjectIntensity revision - 2
     What did you call the greyscale images you want to measure?    CorrActin
     What did you call the objects that you want to measure?    Nuclei
        Cells
        Cytoplasm
        Do not use
        Do not use
        Do not use

Module #15: MeasureObjectIntensity revision - 2
     What did you call the greyscale images you want to measure?    CorrTub
     What did you call the objects that you want to measure?    Nuclei
        Cells
        Cytoplasm
        Do not use
        Do not use
        Do not use

Module #16: MeasureObjectNeighbors revision - 5
     What did you call the objects whose neighbors you want to measure?    Cells
     Objects are considered neighbors if they are within this distance, in pixels. If you want your objects to be touching before you count neighbors (for instance, in an image of tissue), use the ExpandOrShrink module to expand your objects:    3
     What do you want to call the objects colored by number of neighbors, which are compatible for converting to a color image using the Convert To Image and Save Images modules?    Do not use
     What do you want to call the image of the objects with grayscale values corresponding to the number of neighbors, which is compatible for saving in .mat format using the Save Images module for further analysis in Matlab?    Do not use
     This text is left for consistency with prior versions. Any saved settings shown to the right are not used.    n/a

Module #17: MeasureObjectNeighbors revision - 5
     What did you call the objects whose neighbors you want to measure?    Cells
     Objects are considered neighbors if they are within this distance, in pixels. If you want your objects to be touching before you count neighbors (for instance, in an image of tissue), use the ExpandOrShrink module to expand your objects:    10
     What do you want to call the objects colored by number of neighbors, which are compatible for converting to a color image using the Convert To Image and Save Images modules?    Do not use
     What do you want to call the image of the objects with grayscale values corresponding to the number of neighbors, which is compatible for saving in .mat format using the Save Images module for further analysis in Matlab?    Do not use
     This text is left for consistency with prior versions. Any saved settings shown to the right are not used.    n/a

Module #18: MeasureObjectNeighbors revision - 5
     What did you call the objects whose neighbors you want to measure?    Nuclei
     Objects are considered neighbors if they are within this distance, in pixels. If you want your objects to be touching before you count neighbors (for instance, in an image of tissue), use the ExpandOrShrink module to expand your objects:    10
     What do you want to call the objects colored by number of neighbors, which are compatible for converting to a color image using the Convert To Image and Save Images modules?    Do not use
     What do you want to call the image of the objects with grayscale values corresponding to the number of neighbors, which is compatible for saving in .mat format using the Save Images module for further analysis in Matlab?    Do not use
     This text is left for consistency with prior versions. Any saved settings shown to the right are not used.    n/a

Module #19: MeasureObjectNeighbors revision - 5
     What did you call the objects whose neighbors you want to measure?    Nuclei
     Objects are considered neighbors if they are within this distance, in pixels. If you want your objects to be touching before you count neighbors (for instance, in an image of tissue), use the ExpandOrShrink module to expand your objects:    20
     What do you want to call the objects colored by number of neighbors, which are compatible for converting to a color image using the Convert To Image and Save Images modules?    Do not use
     What do you want to call the image of the objects with grayscale values corresponding to the number of neighbors, which is compatible for saving in .mat format using the Save Images module for further analysis in Matlab?    Do not use
     This text is left for consistency with prior versions. Any saved settings shown to the right are not used.    n/a

Module #20: MeasureTexture revision - 2
     What did you call the greyscale images you want to measure?    CorrDAPI
     What did you call the objects that you want to measure?    Nuclei
        Do not use
        Do not use
        Do not use
        Do not use
        Do not use
     What is the scale of texture? A list of texture scales can be specified, separated by commas.    10

Module #21: MeasureTexture revision - 2
     What did you call the greyscale images you want to measure?    CorrActin
     What did you call the objects that you want to measure?    Nuclei
        Cells
        Cytoplasm
        Do not use
        Do not use
        Do not use
     What is the scale of texture? A list of texture scales can be specified, separated by commas.    10

Module #22: MeasureTexture revision - 2
     What did you call the greyscale images you want to measure?    CorrTub
     What did you call the objects that you want to measure?    Nuclei
        Cells
        Cytoplasm
        Do not use
        Do not use
        Do not use
     What is the scale of texture? A list of texture scales can be specified, separated by commas.    10

Module #23: MeasureTexture revision - 2
     What did you call the greyscale images you want to measure?    CorrDAPI
     What did you call the objects that you want to measure?    Nuclei
        Do not use
        Do not use
        Do not use
        Do not use
        Do not use
     What is the scale of texture? A list of texture scales can be specified, separated by commas.    3

Module #24: MeasureTexture revision - 2
     What did you call the greyscale images you want to measure?    CorrActin
     What did you call the objects that you want to measure?    Nuclei
        Cells
        Cytoplasm
        Do not use
        Do not use
        Do not use
     What is the scale of texture? A list of texture scales can be specified, separated by commas.    3

Module #25: MeasureTexture revision - 2
     What did you call the greyscale images you want to measure?    CorrTub
     What did you call the objects that you want to measure?    Nuclei
        Cells
        Cytoplasm
        Do not use
        Do not use
        Do not use
     What is the scale of texture? A list of texture scales can be specified, separated by commas.    3

Module #26: SaveImages revision - 14
     What did you call the images you want to save? If you would like to save an entire figure, enter the module number here    CellOutline
     Which images' original filenames do you want use as a prefix for these new images' filenames? Your choice MUST be images loaded directly with a Load module. Alternately, type N to use sequential numbers for the file names, or type =DesiredFilename to use the single file name you specify (replace DesiredFilename with the name you actually want, or a token if FileNameMetadata was used) for all files (this is *required* when saving an avi movie).    DAPI
     Enter text or metadata tokens to append to the image name, type N to use sequential numbers, or leave "Do not use" to not append anything.    Outline
     In what file format do you want to save images (figures must be saved as fig, which is only openable in Matlab)?    png
     Enter the pathname to the directory where you want to save the images.  Type period (.) for default output directory or ampersand (&) for the directory of the original image. If this directory does not exist, it will be created automatically.    .
     Enter the bit depth at which to save the images (Note: some image formats do not support saving at a bit depth of 12 or 16; see Matlab's imwrite function for more details.)    8
     Do you want to always check whether you will be overwriting a file when saving images?    No
     At what point in the pipeline do you want to save the image? When saving in avi (movie) format, choose Every cycle.    Every cycle
     If you are saving in avi (movie) format, do you want to save the movie only after the last cycle is processed (enter 'L'), or after every Nth cycle (1,2,3...)? Saving movies is time-consuming. See the help for this module for more details.    L
     Do you want to rescale the images to use a full 8 bit (256 graylevel) dynamic range (Y or N)? Use the RescaleIntensity module for other rescaling options.    No
     For grayscale images, specify the colormap to use (see help). This is critical for movie (avi) files. Choosing anything other than gray may degrade image quality or result in image stretching.    gray
     Enter any optional parameters here ('Quality',1 or 'Quality',100 etc.) or leave "Do not use" for no optional parameters.    Do not use
     (If "Every cycle" chosen for When To Save) Update file names within CellProfiler? See help for details.    Yes
     Do you want to create subdirectories in the output directory to match the input image directory structure? (Note: This option cannot be used with the "N" or "=DesiredFilename" option above)    No
     Warning! It is possible to overwrite existing files using this module!    n/a

Module #27: ExportToDatabase revision - 10
     What type of database do you want to use?    MySQL
     For MySQL only, what is the name of the database to use?    2007_05_16_HCS_AstraZeneca
     What prefix should be used to name the tables in the database (should be unique per experiment, or leave "Do not use" to have generic Per_Image and Per_Object tables)?  An underscore will be added to the end of the prefix automatically. If a FileNameMetadata module was used, a regular expression may be inserted here.    Week1
     What prefix should be used to name the SQL files?    SQL_
     Enter the directory where the SQL files are to be saved.  Type period (.) to use the default output folder.    .
     Which per-image statistics do you want to be calculate?  Select "Do not use" to omit.    Mean
         Standard deviation
         Median
     Which objects do you want to export? Use "All objects" in this first box to export all objects (including 'Image'), or select the objects you want to export in this and the following boxes. Use "Do not use" to ignore.     Image
        Do not use
        Do not use
        Do not use
        Do not use
        Do not use
        Do not use
     Do you want to create a Per_Well table? (NOTE: You must use a FileNameMetaData module to create a Per_Well table; See Help for details.)    No
     Which token uniquely specifies your Plate? (Select 'Do not use' if you only have one plate)    Do not use
     Which token uniquely specifies your Well?     Do not use
     Do you want to create a CellProfiler Analyst properties file?    Yes - Both V1.0 and V2.0 format

Module #28: CreateBatchFiles revision - 8
     What is the path to the folder where the batch control file (Batch_data.mat) will be saved? Leave a period (.) to use the default output folder.    .
     LOCAL MACHINE'S root path (omitting trailing slashes). Leave a period (.) if LOCAL and CLUSTER root paths are the same. If your image and output folder paths are different, enter the input then the output path separated by a comma.    .
     CLUSTER MACHINE'S root path (omitting trailing slashes). Leave a period (.) if LOCAL and CLUSTER root paths are the same. See above for entering multiple paths.    .
     Note: This module must be the last one in the analysis pipeline.    n/a
