Galaxy | Tool Preview

DisplayDataOnImage (version 3.1.9+galaxy1)

Select the input CellProfiler pipeline:

Display object or image measurements?:

Enter the name of the input objects:

Enter the name of the objects identified by some other tool used upstream in the workflow (such as IdentifyPrimaryObjects or IdentifySecondaryObjects).

Measurement category:

The measurement will be made by some other tool used upstream in the workflow on either the whole image or on the objects you selected.

Measurement:

Display background image?:

Usually, you will want to see the image context for the measurements, but it may be useful to save just the overlay of the text measurements and composite the overlay image and the original image later.

Enter the name of the image on which to display the measurements:

Display mode:

If you choose Text, DisplayDataOnImage will display the numeric value on top of each object. If you choose Color, DisplayDataOnImage will convert the image to grayscale, if necessary, and display the portion of the image within each object using a hue that indicates the measurement value relative to the other objects in the set using the default color map.

Text color:

Font size (points):

Number of decimals:

Annotation offset (in pixels):

Normally, the text is placed at the object (or image) center, which can obscure relevant features of the object. This setting adds a specified offset to the text, in a random direction.

Name the output image that has the measurements displayed:

Image elements to save:

This setting controls the level of annotation on the image:
- Image: Saves the image with the overlaid measurement annotations.
- Figure: Adds a title and other decorations.
- Axes: Adds axes with tick marks and image coordinates.

What it does

This module displays either a single image measurement on an image of your choosing, or one object measurement per object on top of every object in an image. The display itself is an image which you can save to a file using SaveImages.

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.