Galaxy |

MeasureObjectSizeShape (version 3.1.9+galaxy1)

Select the input CellProfiler pipeline:

new objects

new object 0

Calculate the Zernike features?:

Select 'Yes' to calculate the Zernike shape features. Because the first 10 Zernike polynomials (from order 0 to order 9) are calculated, this operation can be time-consuming if the image contains a lot of objects. Select 'No' if you are measuring 3D objects with this module.

What it does

Given an image with identified objects (e.g., nuclei or cells), this module extracts area and shape features of each one. Note that these features are only reliable for objects that are completely inside the image borders, so you may wish to exclude objects touching the edge of the image using Identify settings for 2D objects, or by applying FilterObjects downstream.

The display window for this module shows per-image aggregates for the per-object measurements. If you want to view the per-object measurements themselves, you will need to use an Export module to export them, or use DisplayDataOnImage to display the object measurements of choice overlaid on an image of choice.

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.