Galaxy |

OverlayOutlines (version 3.1.9+galaxy1)

Select the input CellProfiler pipeline:

Display outlines on a blank image?:

Outline display mode:

Specify how to display the outline contours around your objects. Color: outlines produce a clearer display for images where the cell borders have a high intensity, but take up more space in memory. Grayscale: outlines are displayed with either the highest possible intensity or the same intensity as the brightest pixel in the image.

Outlines

Outline 0

Name the output image:

How to outline:

Specify how to mark the boundaries around an object: Inner: outline the pixels just inside of objects, leaving background pixels untouched. Outer: outline pixels in the background around object boundaries. When two objects touch, their boundary is also marked. Thick: any pixel not completely surrounded by pixels of the same label is marked as a boundary. This results in boundaries that are 2 pixels thick.

What it does

This module places outlines of objects on any desired image (grayscale, color, or blank). The resulting image can be saved using the SaveImages 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.