What it does

This module allows you to take previously identified objects and convert them into an image according to a colormap you select, which can then be saved with the SaveImages module.

For the colormap, you have the following options:

• Color: Allows you to choose a colormap that will produce jumbled colors for your objects.
• Binary (black & white): All object pixels will be assigned 1 and all background pixels will be assigned 0, creating a binary image.
• Grayscale: Assigns all background pixels to 0 and each object a different number from 1 to 255 (the maximum value that you can put in an 8-bit integer) and numbers all pixels in each object with the object’s number. This creates an image where objects in the top left corner of the image are very dark and where the colors progress to white toward the bottom right corner of the image.
• uint16: Assigns all background pixels to 0 and each object a different number from 1 to 65535 (the maximum value that you can put in a 16-bit integer) and numbers all pixels in each object with the object’s number. This creates an image where objects in the top left corner of the image are very dark and where the colors progress to white toward the bottom right corner of the image (though this can usually only be seen in a scientific image viewer since standard image viewers only handle 8-bit images).

You can choose Color with a Gray colormap to produce jumbled gray objects.

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.