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MeasureImageQuality (version 3.1.9+galaxy1)

Select the input CellProfiler pipeline:

Calculate metrics for which images?:

Image names are separated by comma and correspond to the values in the section NameAndType of the 'Starting module' tool.

Include the image rescaling value?:

Select 'Yes' to add the image’s rescaling value as a quality control metric. This value is recorded only for images loaded using the Input modules. This is useful in confirming that all images are rescaled by the same value, given that some acquisition device vendors may output this value differently.

Calculate blur metrics?:

Calculate intensity metrics?:

Select 'Yes' to calculate image-based intensity measures, namely the mean, maximum, minimum, standard deviation and median absolute deviation of pixel intensities. These measures are identical to those calculated by MeasureImageIntensity.

Calculate saturation metrics:

Select 'Yes' to calculate the saturation metrics PercentMaximal and PercentMinimal, i.e., the percentage of pixels at the upper or lower limit of each individual image. For this calculation, the hard limits of 0 and 1 are not used because images often have undergone some kind of transformation such that no pixels ever reach the absolute maximum or minimum of the image format. Given the noise typical in images, both these measures should be a low percentage but if the images were saturated during imaging, a higher than usual PercentMaximal will be observed, and if there are no objects, the PercentMinimal value will increase.

Calculate thresholds?:

Automatically calculate a suggested threshold for each image. One indicator of image quality is that these threshold values lie within a typical range. Outlier images with high or low thresholds often contain artifacts.

Use all thresholding methods?:

Select 'Yes' to calculate thresholds using all the available methods. Only the global methods are used. While most methods are straightfoward, some methods have additional parameters that require special handling:
- Otsu: Thresholds for all combinations of class number, minimization parameter and middle class assignment are computed.
- Mixture of Gaussians (MoG): Thresholds for image coverage fractions of 0.05, 0.25, 0.75 and 0.95 are computed. See the IdentifyPrimaryObjects module for more information on thresholding methods.

What it does

This tool collects measurements indicating possible image aberrations, e.g., blur (poor focus), intensity, saturation (i.e., the percentage of pixels in the image that are at/near the maximum possible value, and at/near the minimum possible value). Details and guidance for each of these measures is provided in the settings help. Please note that for best results, this module should be applied to the original raw images, rather than images that have already been corrected for illumination.

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.