Available Features

CellProfiler Features

  • intensity

    Measures several intensity features for identified objects. Parameters:

    1. c: Channel index.

  • granularity

    Outputs spectra of size measurements of the textures in the image. Parameters:

    1. c: Channel index.

  • intensity-distribution

    Measures radial intensity features for identified objects. Parameters:

    1. c: Channel index.

    2. bins: Number of bins to measure the distribution (default 4)

  • intensity-distribution-zernike

    Measures zernike intensity features for identified objects. Parameters:

    1. c: Channel index.

    2. moment: Maximum zernike moment (default 9)

  • haralick

    Measures the degree and nature of textures within objects to quantify their roughness and smoothness. Parameters:

    1. c: Channel index.

    2. scale: Number of pixels included in gray-level co-occurence matrix (Default 3).

  • sizeshape

    Measures several area and shape features of identified objects.

  • neighbors

    Calculates how many neighbors each object has and records various properties about the neighbors’ relationships, including the percentage of an object’s edge pixels that touch a neighbor.

  • colocalization

    Measures the colocalization and correlation between intensities in different channels on a pixel-by-pixel basis within identified objects. Parameters:

    1. c1: First channel index.

    2. c2: Second channel index.

Other Features

  • pftas

    Parameter-free threshold adjacency statistics. Outputs 54 features. Reference: Fast automated cell phenotype image classification Parameters:

    1. c: Channel index.

  • correlation-pearson-box

    Pearson correlation coefficient between two channels in the label bounding box. Typically used to measure nuclei alignment quality of ISS and phenotype images. Parameters:

    1. c1: First channel index.

    2. c2: Second channel index.

  • intersects-boundary

    Determines whether a label intersects a stitch boundary. Parameters:

    1. c: Channel index.

  • spots

    Counts the number of spots in a FISH image. Parameters:

    1. c: Channel index.

    2. min peak_distance: Minimum number of pixels separating peaks (default 3).

    3. radius: Radius of the disk footprint used for non-maximum suppression in peak_local_max (default 3).

Shortcuts

Use * for all channels. Example: intensity_*, colocalization_*_*.

Include a comma separated list of channel indices (0-based) to include. Example: intensity_0,1,2,6.

Specify a range of channel indices using start:stop:step. Example: colocalization_0_1:10:2.

Notes

Feature names are case insensitive (intensity == Intensity) and hyphens in feature names are ignored (intensitydistribution == intensity-distribution)