Commits

Marinka Zitnik committed e1d6c18

aligning images and updated patch tracking

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Files changed (1)

     Channel number:1
     Rescale intensities?:Yes
 
-IdentifyPrimaryObjects:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'Identify the cells from the original image.\'\x5D]
-    Select the input image:OrigImage
+LoadSingleImage:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D]
+    Input image file location:Default Input Folder\x7CNone
+    Filename of the image to load (Include the extension, e.g., .tif):\\g<Movie>-1.tif
+    Load as images or objects?:Images
+    Name the image that will be loaded:FirstToAlign
+    Name this loaded object:Nuclei
+    Retain outlines of loaded objects?:No
+    Name the outlines:NucleiOutlines
+    Rescale intensities?:Yes
+
+Align:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D]
+    Select the alignment method:Normalized Cross Correlation
+    Crop mode:Keep size
+    Select the first input image:FirstToAlign
+    Name the first output image:AlignedFirst
+    Select the second input image:OrigImage
+    Name the second output image:AlignedOrigImage
+
+IdentifyPrimaryObjects:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'Identify the cells from the original image.\'\x5D]
+    Select the input image:AlignedOrigImage
     Name the primary objects to be identified:Cell
     Typical diameter of objects, in pixel units (Min,Max):20,65
     Discard objects outside the diameter range?:Yes
     Maximum number of objects:500
     Select the measurement to threshold with:None
 
-TrackObjects:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D]
+TrackObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D]
     Choose a tracking method:Overlap
     Select the objects to track:Cell
     Select object measurement to use for tracking:None
     Maximum merge score:50
     Maximum gap:5
 
-ExpandOrShrinkObjects:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D]
+ExpandOrShrinkObjects:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D]
     Select the input objects:Cell
     Name the output objects:ExtendedCell
     Select the operation:Expand objects by a specified number of pixels
     Retain the outlines of the identified objects for use later in the pipeline (for example, in SaveImages)?:No
     Name the outline image:ShrunkenNucleiOutlines
 
-EnhanceOrSuppressFeatures:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'Use filtering to enhance the speckles in the image. The feature size setting should be specified to be at least as large as the largest feature to be enhanced.\'\x5D]
-    Select the input image:OrigImage
+EnhanceOrSuppressFeatures:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'Use filtering to enhance the speckles in the image. The feature size setting should be specified to be at least as large as the largest feature to be enhanced.\'\x5D]
+    Select the input image:AlignedOrigImage
     Name the output image:EnhancedOrig
     Select the operation:Enhance
     Feature size:3
     Feature type:Speckles
     Range of hole sizes:1,10
 
-MaskImage:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\'Mask the enhanced original image using the cell objects.\'\x5D]
+MaskImage:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\'Mask the enhanced original image using the cell objects.\'\x5D]
     Select the input image:EnhancedOrig
     Name the output image:MaskedOrig
     Use objects or an image as a mask?:Objects
     Select image for mask:None
     Invert the mask?:No
 
-IdentifyPrimaryObjects:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'Identify the actin pathces using per-object thresholding to compute a threshold for each individual cell object. Some manual adjustment of the smoothing filter size and maxima supression distance is required to optimize segmentation.\'\x5D]
+IdentifyPrimaryObjects:[module_num:9|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'Identify the actin pathces using per-object thresholding to compute a threshold for each individual cell object. Some manual adjustment of the smoothing filter size and maxima supression distance is required to optimize segmentation.\'\x5D]
     Select the input image:MaskedOrig
     Name the primary objects to be identified:Patch
     Typical diameter of objects, in pixel units (Min,Max):2,20
     Maximum number of objects:500
     Select the measurement to threshold with:None
 
-RelateObjects:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D]
+RelateObjects:[module_num:10|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D]
     Select the input child objects:Patch
     Select the input parent objects:Cell
     Calculate distances?:Both
     Calculate distances to other parents?:No
     Parent name:None
 
-MeasureObjectIntensity:[module_num:9|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D]
+MeasureObjectIntensity:[module_num:11|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D]
     Hidden:1
-    Select an image to measure:OrigImage
+    Select an image to measure:AlignedOrigImage
     Select objects to measure:Patch
 
-TrackObjects:[module_num:10|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D]
+TrackObjects:[module_num:12|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D]
     Choose a tracking method:Distance
     Select the objects to track:Patch
     Select object measurement to use for tracking:None
-    Maximum pixel distance to consider matches:50
+    Maximum pixel distance to consider matches:10
     Select display option:Color and Number
     Save color-coded image?:No
     Name the output image:TrackedCells
     Maximum merge score:50
     Maximum gap:5
 
-ExportToSpreadsheet:[module_num:11|svn_version:\'Unknown\'|variable_revision_number:7|show_window:False|notes:\x5B\'Save computed measures to spreadsheet file. \'\x5D]
+SaveImages:[module_num:13|svn_version:\'Unknown\'|variable_revision_number:7|show_window:False|notes:\x5B\x5D]
+    Select the type of image to save:Image
+    Select the image to save:AlignedOrigImage
+    Select the objects to save:None
+    Select the module display window to save:None
+    Select method for constructing file names:Sequential numbers
+    Select image name for file prefix:OrigImage
+    Enter file prefix:\\g<Movie>-aligned-
+    Do you want to add a suffix to the image file name?:No
+    Text to append to the image name:
+    Select file format to use:tif
+    Output file location:Default Output Folder\x7CNone
+    Image bit depth:16
+    Overwrite existing files without warning?:Yes
+    Select how often to save:Every cycle
+    Rescale the images? :No
+    Save as grayscale or color image?:Grayscale
+    Select colormap:gray
+    Store file and path information to the saved image?:No
+    Create subfolders in the output folder?:No
+
+ExportToSpreadsheet:[module_num:14|svn_version:\'Unknown\'|variable_revision_number:7|show_window:False|notes:\x5B\'Save computed measures to spreadsheet file. \'\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?:No