Galaxy | Tool Preview

EnhanceOrSuppressFeatures (version 3.1.9+galaxy1)
Enhance produces an image whose intensity is largely composed of the features of interest and Supress produces an image with the features largely removed.
- Speckles: A speckle is an area of enhanced intensity relative to its immediate neighborhood. This option enhances speckles using a white tophat filter, which is the image minus the morphological grayscale opening of the image. The opening operation first suppresses the speckles by applying a grayscale erosion to reduce everything within a given radius to the lowest value within that radius, then uses a grayscale dilation to restore objects larger than the radius to an approximation of their former shape. The white tophat filter enhances speckles by subtracting the effects of opening from the original image.
- Neurites: Neurites are taken to be long, thin features of enhanced intensity. Choose this option to enhance the intensity of the neurites using the Line structures or Tubeness methods described in a later setting.
- Dark holes: This option uses morphological reconstruction (the rolling-ball algorithm) to identify dark holes within brighter areas, or brighter ring shapes. The image is inverted so that the dark holes turn into bright peaks. The image is successively eroded and the eroded image is reconstructed at each step, resulting in an image that is missing the peaks. Finally, the reconstructed image is subtracted from the previous reconstructed image. This leaves circular bright spots with a radius equal to the number of iterations performed.
- Circles: This option calculates the circular Hough transform of the image at the diameter given by the feature size. The Hough transform will have the highest intensity at points that are centered within a ring of high intensity pixels where the ring diameter is the feature size. You may want to use the EnhanceEdges module to find the edges of your circular object and then process the output by enhancing circles. You can use IdentifyPrimaryObjects to find the circle centers and then use these centers as seeds in IdentifySecondaryObjects to find whole, circular objects using a watershed.
- Texture: This option produces an image whose intensity is the variance among nearby pixels. The method weights pixel contributions by distance using a Gaussian to calculate the weighting. You can use this method to separate foreground from background if the foreground is textured and the background is not.
- DIC: This method recovers the optical density of a DIC image by integrating in a direction perpendicular to the shear direction of the image.
Enter the diameter of the largest speckle, the width of the circle, or the width of the neurites to be enhanced or suppressed, which will be used to calculate an appropriate filter size.
Speckles can use a fast or slow algorithm to find speckles.
- Fast: Select this option for speckles that have a large radius (greater than 10 pixels) and need not be exactly circular.
- Slow: Use for speckles of small radius.

What it does

This tool enhances or suppresses the intensity of certain pixels relative to the rest of the image, by applying image processing filters to the image. It produces a grayscale image in which objects can be identified using an Identify module.

Input

Existing CellProfiler pipeline file (.cppipe) or generated by linking CellProfiler tools.

Output

The input CellProfiler pipeline file (.cppipe) in addition to the settings of this module.

IMPORTANT

The first tool in a CellProfiler workflow has to be Starting modules and the last one CellProfiler. You can also execute the entire pipeline with the final CellProfiler tool, in which you feed in the images you want to process as well.