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MaskImage (version 3.1.9+galaxy1)

Select the input CellProfiler pipeline:

Enter the name of the input image:

Enter the name of the resulting image:

Use objects or an image as a mask?:

You can mask an image in two ways:
- Objects: Using objects created by another module (for instance IdentifyPrimaryObjects). The module will mask out all parts of the image that are not within one of the objects (unless you invert the mask).
- Image: Using a binary image as the mask, where black portions of the image (false or zero-value pixels) will be masked out. If the image is not binary, the module will use all pixels whose intensity is greater than 0.5 as the mask’s foreground (white area). You can use Threshold instead to create a binary image with finer control over the intensity choice.

Enter the name objects to mask the input image:

Invert the mask?:

This option reverses the foreground/background relationship of the mask.
- Select "No" to produce the mask from the foreground (white portion) of the masking image or the area within the masking objects.
- Select "Yes" to instead produce the mask from the background (black portions) of the masking image or the area outside the masking objects.

What it does

This tool masks an image so you can use the mask downstream in the pipeline. The masked image is based on the original image and the masking object or image that is selected. If using a masking image, the mask is composed of the foreground (white portions); if using a masking object, the mask is composed of the area within the object. Note that the image created by this tool for further processing downstream is grayscale. If a binary mask is desired in subsequent tools, use the Threshold tool instead of MaskImage.

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.