straightens untangled worms.
uses the objects produced by UntangleWorms
to create images and objects of straight worms from the angles and control points as computed by UntangleWorms
. The resulting images can then be uniformly analyzed to find features that correlate with position in an ideal representation of the worm, such as the head or gut.
StraightenWorms works by calculating a transform on the image that translates points in the image to points on the ideal worm. UntangleWorms idealizes a worm as a series of control points that define the worm's shape and length. The training set contains measurements of the width of an ideal worm at each control point. Together, these can be used to reconstruct the worm's shape and correlate between the worm's location and points on the body of an ideal worm.
StraightenWorms produces objects representing the straight worms and images representing the intensity values of a source image mapped onto the straight worms. The objects and images can then be used to compute measurements using any of the object measurement modules, for instance, MeasureTexture.
The module can be configured to make intensity measurements on parts of the worm, dividing the worm up into pieces of equal width and/or height. Measurements are made longitudally in stripes from head to tail and transversely in segments across the width of the worm. Longitudinal stripes are numbered from left to right and transverse segments are numbered from top to bottom. The module will divide the worm into a checkerboard of sections if configured to measure more than one longitudinal stripe and transverse segment. These are numbered by longitudinal stripe number, then transverse segment number. For instance, "Worm_MeanIntensity_GFP_L2of3_T1of4", is a measurement of the mean GFP intensity of the center stripe (second of 3 stripes) of the topmost band (first of four bands). Measurements of longitudinal stripes are designated as "T1of1" indicating that the whole worm is one transverse segment. Likewise measurements of transverse segments are designated as "L1of1" indicating that there is only one longitudinal stripe. Both mean intensity and standard deviation of intensity are measured per worm sub-area.
While StraightenWorms can straighten a color image, the module needs a grayscale image to make its intensity measurements. For a color image, the red, green and blue channels are averaged to yield a grayscale image. The intensity measurements are then made on that grayscale image.
- Location_X, Location_Y: The pixel (X,Y) coordinates of the primary object centroids. The centroid is calculated as the center of mass of the binary representation of the object.
- Worm_MeanIntensity: The average pixel intensity within a worm.
- Worm_StdIntensity: The standard deviation of the pixel intensities within a worm.
- Peng H, Long F, Liu X, Kim SK, Myers EW (2008) "Straightening Caenorhabditis elegans images." Bioinformatics, 24(2):234-42.(link)
- Wählby C, Kamentsky L, Liu ZH, Riklin-Raviv T, Conery AL, O'Rourke EJ, Sokolnicki KL, Visvikis O, Ljosa V, Irazoqui JE, Golland P, Ruvkun G, Ausubel FM, Carpenter AE (2012). "An image analysis toolbox for high-throughput C. elegans assays." Nature Methods 9(7): 714-716. (link)
Select the input untangled worm objects
This is the name of the objects produced by the
UntangleWorms module. StraightenWorms can use
either the overlapping or non-overlapping objects as input. It
will use the control point measurements associated with the objects
to reconstruct the straight worms. You can also use objects
saved from a previous run and loaded via the Input modules, objects
edited using EditObjectsManually or objects from one
of the Identify modulues. StraightenWorms
will recalculate the control points for these images.
Name the output straightened worm objects
This is the name that will be given to the straightened
worm objects. These objects can then be used in a subsequent
This setting determines the width of the image of each
worm. The width should be set to at least the maximum width of
any untangled worm, but can be set to be larger to include the
worm's background in the straightened image.
Training set file location
Select the folder containing the training set to be loaded.
You can choose among the following options which are common to all file input/output
- Default Input Folder: Use the default input folder.
- Default Output Folder: Use from the default output folder.
- Elsewhere...: Use a particular folder you specify.
- Default input directory sub-folder: Enter the name of a subfolder of
the default input folder or a path that starts from the default input folder.
- Default output directory sub-folder: Enter the name of a subfolder of
the default output folder or a path that starts from the default output folder.
Elsewhere and the two sub-folder options all require you to enter an additional
path name. You can use an absolute path (such as "C:\imagedir\image.tif" on a PC) or a
relative path to specify the file location relative to a directory):
- Use one period to represent the current directory. For example, if you choose
Default Input Folder sub-folder, you can enter "./MyFiles" to look in a
folder called "MyFiles" that is contained within the Default Input Folder.
- Use two periods ".." to move up one folder level. For example, if you choose
Default Input Folder sub-folder, you can enter "../MyFolder" to look in a
folder called "MyFolder" at the same level as the Default Input Folder.
An additional option is the following:
- URL: Use the path part of a URL. For instance, your
training set might be hosted at
To access this file, you would choose URL and enter
as the path location.
Training set file name
This is the name of the training set file.
Measure intensity distribution?
Select Yes to divide a worm into sections
and measure the intensities of each section in each of the
straightened images. These measurements can help classify
phenotypes if the staining pattern across the segments differs
Number of transverse segments
(Only used if intensities are measured)
This setting controls the number of segments measured, dividing
the worm longitudally into transverse segments starting at the head
and ending at the tail.
These measurements might be used to identify a phenotype in which
a stain is localized longitudally, for instance, in the head.
Set the number of vertical segments to 1 to only measure intensity
in the horizontal direction.
Number of longitudinal stripes
(Only used if intensities are measured)
This setting controls the number of stripes measured, dividing
the worm transversely into areas that run longitudally. These
measurements might be used to identify a phenotype in which a
stain is localized transversely, for instance in the gut of the
Set the number of horizontal stripes to 1 to only measure intensity
in the vertical direction.
(Only used if intensities are measured)
StraightenWorms can align worms so that the brightest
half of the worm (the half with the highest mean intensity) is
at the top of the image or at the bottom of the image. This
can be used to align all worms similarly if some feature,
such as the larynx, is stained and is always at the same end
of the worm. Choose Top brightest if the brightest part of the
worm should be at the top of the image, Bottom brightest if the
brightest part of the worm should be at the bottom or
Do not align if the worm should not be aligned.
Choose Flip manually to bring up an editor for every
cycle that allows you to choose the orientation of each worm.
(Only used if aligning worms)
This is the image whose intensity will be used to align the worms.
You must use one of the straightened images below.
Select an input image to straighten
This is the name of an image that will be straightened
similarly to the worm. The straightened image and objects can
then be used in subsequent modules such as
Name the output straightened image
This is the name that will be given to the image
of the straightened worms.