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

SVN version number: 9405
Pixel Size: 1

Pipeline:
	LoadText
	LoadImageDirectory
	LoadImageDirectory
	LoadImageDirectory
	LoadImageDirectory
	SmoothOrEnhance
	SmoothOrEnhance
	SmoothOrEnhance
	SmoothOrEnhance
	SaveImages
	SaveImages
	SaveImages
	SaveImages
	CreateBatchFiles

Module #1: LoadText revision - 2
     What is the file containing the text that you want to load?    finaltxt.txt
     What would you like to call the loaded text?    QCFlag
     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.    /imaging/analysis/2007_05_16_HCS_AstraZeneca/2008_10_28_AZ_Drives/MorphologyAssay/Week1QC

Module #2: LoadImageDirectory revision - 2
     Enter the pathname to the folders containing images:    .
     Enter the text that the folders have in common:    Week1
     Analyze all subfolders within each folder?    No
     How do you want to load these files?    Exact match
     Enter the text that one type of file has in common:    _w1
     What kind of projection would you like to make?    Average
     Would you like to check images for a QCFlag (loaded earlier in a load text module) and bypass images possessing a flag in calculation of the illumination correction function?    Yes
     What did you call the loaded text that contains the QCFlag? (This is only used for QCFlag=YES)    QCFlag
     How many images are in each directory you are loading? (This is only used for QCFlag=YES)    960
     How many channels are there each directory you are loading? (This is only used for QCFlag=YES)    4
     What do you want to call the projected image?    IllumDAPI

Module #3: LoadImageDirectory revision - 2
     Enter the pathname to the folders containing images:    .
     Enter the text that the folders have in common:    Week1
     Analyze all subfolders within each folder?    Yes
     How do you want to load these files?    Exact match
     Enter the text that one type of file has in common:    _w2
     What kind of projection would you like to make?    Average
     Would you like to check images for a QCFlag (loaded earlier in a load text module) and bypass images possessing a flag in calculation of the illumination correction function?    Yes
     What did you call the loaded text that contains the QCFlag? (This is only used for QCFlag=YES)    QCFlag
     How many images are in each directory you are loading? (This is only used for QCFlag=YES)    960
     How many channels are there each directory you are loading? (This is only used for QCFlag=YES)    4
     What do you want to call the projected image?    IllumTubulin

Module #4: LoadImageDirectory revision - 2
     Enter the pathname to the folders containing images:    .
     Enter the text that the folders have in common:    Week1
     Analyze all subfolders within each folder?    Yes
     How do you want to load these files?    Exact match
     Enter the text that one type of file has in common:    _w3
     What kind of projection would you like to make?    Average
     Would you like to check images for a QCFlag (loaded earlier in a load text module) and bypass images possessing a flag in calculation of the illumination correction function?    Yes
     What did you call the loaded text that contains the QCFlag? (This is only used for QCFlag=YES)    QCFlag
     How many images are in each directory you are loading? (This is only used for QCFlag=YES)    960
     How many channels are there each directory you are loading? (This is only used for QCFlag=YES)    4
     What do you want to call the projected image?    IllumCellMask

Module #5: LoadImageDirectory revision - 2
     Enter the pathname to the folders containing images:    .
     Enter the text that the folders have in common:    Week1
     Analyze all subfolders within each folder?    Yes
     How do you want to load these files?    Exact match
     Enter the text that one type of file has in common:    _w4
     What kind of projection would you like to make?    Average
     Would you like to check images for a QCFlag (loaded earlier in a load text module) and bypass images possessing a flag in calculation of the illumination correction function?    Yes
     What did you call the loaded text that contains the QCFlag? (This is only used for QCFlag=YES)    QCFlag
     How many images are in each directory you are loading? (This is only used for QCFlag=YES)    960
     How many channels are there each directory you are loading? (This is only used for QCFlag=YES)    4
     What do you want to call the projected image?    IllumActin

Module #6: SmoothOrEnhance revision - 5
     What did you call the image to be smoothed?    IllumDAPI
     What do you want to call the smoothed image?    CorrDAPI
     Enter the smoothing method you would like to use.    Fit Polynomial
     If you choose any setting besides 'Fit Polynomial' as your smoothing method, please specify the approximate width of the objects in your image (in pixels). This will be used to calculate an adequate filter size. If you don't know the width of your objects, you can use the ShowOrHidePixelData image tool to find out or leave the word 'Automatic'. For 'Enhance Dark Holes', a range of values may be used, separated by a hyphen.     Automatic
     If you want to use your own filter size (in pixels), please specify it here. Otherwise, leave "Do not use". If you entered a width for the previous variable, this will override it.    Do not use
     Are you using this module to smooth an image that results from processing multiple cycles?  (If so, this module will wait until it sees a flag that the other module has completed its calculations before smoothing is performed).    No
     If you choose 'Smooth Keeping Edges', what spatial filter radius should be used, in pixels? (The approximate size of preserved objects is good)?    16.0
     If you choose 'Smooth Keeping Edges', what intensity-based radius should be used, in intensity units? (Half the intensity step that indicates an edge is good.  Set to 0.0 to calculate from the image.)?    0.1

Module #7: SmoothOrEnhance revision - 5
     What did you call the image to be smoothed?    IllumActin
     What do you want to call the smoothed image?    CorrActin
     Enter the smoothing method you would like to use.    Fit Polynomial
     If you choose any setting besides 'Fit Polynomial' as your smoothing method, please specify the approximate width of the objects in your image (in pixels). This will be used to calculate an adequate filter size. If you don't know the width of your objects, you can use the ShowOrHidePixelData image tool to find out or leave the word 'Automatic'. For 'Enhance Dark Holes', a range of values may be used, separated by a hyphen.     80
     If you want to use your own filter size (in pixels), please specify it here. Otherwise, leave "Do not use". If you entered a width for the previous variable, this will override it.    Do not use
     Are you using this module to smooth an image that results from processing multiple cycles?  (If so, this module will wait until it sees a flag that the other module has completed its calculations before smoothing is performed).    No
     If you choose 'Smooth Keeping Edges', what spatial filter radius should be used, in pixels? (The approximate size of preserved objects is good)?    16.0
     If you choose 'Smooth Keeping Edges', what intensity-based radius should be used, in intensity units? (Half the intensity step that indicates an edge is good.  Set to 0.0 to calculate from the image.)?    0.1

Module #8: SmoothOrEnhance revision - 5
     What did you call the image to be smoothed?    IllumCellMask
     What do you want to call the smoothed image?    CorrCellMask
     Enter the smoothing method you would like to use.    Fit Polynomial
     If you choose any setting besides 'Fit Polynomial' as your smoothing method, please specify the approximate width of the objects in your image (in pixels). This will be used to calculate an adequate filter size. If you don't know the width of your objects, you can use the ShowOrHidePixelData image tool to find out or leave the word 'Automatic'. For 'Enhance Dark Holes', a range of values may be used, separated by a hyphen.     80
     If you want to use your own filter size (in pixels), please specify it here. Otherwise, leave "Do not use". If you entered a width for the previous variable, this will override it.    Do not use
     Are you using this module to smooth an image that results from processing multiple cycles?  (If so, this module will wait until it sees a flag that the other module has completed its calculations before smoothing is performed).    No
     If you choose 'Smooth Keeping Edges', what spatial filter radius should be used, in pixels? (The approximate size of preserved objects is good)?    16.0
     If you choose 'Smooth Keeping Edges', what intensity-based radius should be used, in intensity units? (Half the intensity step that indicates an edge is good.  Set to 0.0 to calculate from the image.)?    0.1

Module #9: SmoothOrEnhance revision - 5
     What did you call the image to be smoothed?    IllumTubulin
     What do you want to call the smoothed image?    CorrTub
     Enter the smoothing method you would like to use.    Fit Polynomial
     If you choose any setting besides 'Fit Polynomial' as your smoothing method, please specify the approximate width of the objects in your image (in pixels). This will be used to calculate an adequate filter size. If you don't know the width of your objects, you can use the ShowOrHidePixelData image tool to find out or leave the word 'Automatic'. For 'Enhance Dark Holes', a range of values may be used, separated by a hyphen.     Automatic
     If you want to use your own filter size (in pixels), please specify it here. Otherwise, leave "Do not use". If you entered a width for the previous variable, this will override it.    Do not use
     Are you using this module to smooth an image that results from processing multiple cycles?  (If so, this module will wait until it sees a flag that the other module has completed its calculations before smoothing is performed).    No
     If you choose 'Smooth Keeping Edges', what spatial filter radius should be used, in pixels? (The approximate size of preserved objects is good)?    16.0
     If you choose 'Smooth Keeping Edges', what intensity-based radius should be used, in intensity units? (Half the intensity step that indicates an edge is good.  Set to 0.0 to calculate from the image.)?    0.1

Module #10: 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    CorrActin
     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).    IllumActin
     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.    Actin
     In what file format do you want to save images (figures must be saved as fig, which is only openable in Matlab)?    mat
     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.    No
     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 #11: 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    CorrDAPI
     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).    IllumDAPI
     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.    DAPI
     In what file format do you want to save images (figures must be saved as fig, which is only openable in Matlab)?    mat
     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.    No
     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 #12: 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    CorrCellMask
     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).    IllumCellMask
     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.    CellMask
     In what file format do you want to save images (figures must be saved as fig, which is only openable in Matlab)?    mat
     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.    No
     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 #13: 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    CorrTub
     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).    IllumTubulin
     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.    Tubulin
     In what file format do you want to save images (figures must be saved as fig, which is only openable in Matlab)?    mat
     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.    No
     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 #14: 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
