cp_measure: Morphological features for imaging data

Do you need to use CellProfiler features, but you want to do it in a programmatic way? Look no more, this package was developed by and for the click-a-phobic scientists.

Preprint

Here is the preprint. Published as a workshop paper for ICML 2025's CODEML.

Please cite using the following .bib entry

@article{munoz2025cpmeasure,
  title={cp\_measure: API-first feature extraction for image-based profiling workflows},
  author={Mu{\~n}oz, Al{\'a}n F and Treis, Tim and Kalinin, Alexandr A and Dasgupta, Shatavisha and Theis, Fabian and Carpenter, Anne E and Singh, Shantanu},
  journal={arXiv preprint arXiv:2507.01163},
  year={2025}
}

Quick overview

Installation

pip install cp-measure

Usage

Featurizer (Recommended for small datasets)

The simplest way to extract all features from an image and its masks:

import numpy as np
from cp_measure.featurizer import featurize

# image: (C, H, W) float array, masks: (N_masks, H, W) integer labels
image = np.random.default_rng(42).random((2, 240, 240))
masks = np.zeros((1, 240, 240), dtype=np.int32)
masks[0, 50:100, 50:100] = 1
masks[0, 150:200, 150:200] = 2

data, columns, rows = featurize(image, masks)
# data:    np.ndarray of shape (n_objects, n_features)
# columns: feature names (e.g. "Area", "Intensity_MeanIntensity__ch0", ...)
# rows:    [(None, "object", 1), (None, "object", 2)]  — (image_id, object_name, label) per row

To customise which features are extracted, or to name your channels and masks, use make_featurizer_config. Channel names are matched positionally to the image's first axis and control how per-channel features are labeled in the output columns (e.g. "Intensity_MeanIntensity__DNA"). If omitted, channels are auto-named ch0, ch1, ...

import numpy as np
from cp_measure.featurizer import featurize, make_featurizer_config

# Recreate variables from previous examples for this block to run in isolation
image = np.random.default_rng(42).random((2, 240, 240))
masks = np.zeros((1, 240, 240), dtype=np.int32)
masks[0, 50:100, 50:100] = 1
masks[0, 150:200, 150:200] = 2

# Disable texture features, name channels explicitly
config = make_featurizer_config(["DNA", "ER"], texture=False)
data, columns, rows = featurize(image, masks, config)

Multiple mask types (e.g. nuclei and cells) are supported by stacking them along the first axis:

import numpy as np
from cp_measure.featurizer import featurize, make_featurizer_config

# Recreate variables from previous examples for this block to run in isolation
image = np.random.default_rng(42).random((2, 240, 240))

config = make_featurizer_config(["DNA", "ER"], objects=["nuclei", "cells"])

masks = np.zeros((2, 240, 240), dtype=np.int32)
masks[0, 50:100, 50:100] = 1    # nucleus 1
masks[1, 40:110, 40:110] = 1    # cell 1
masks[1, 150:200, 150:200] = 2  # cell 2
masks[1, 175:180, 180:210] = 2  # Minor asymmetries on bottom right edge of cells

data, columns, rows = featurize(image, masks, config)
# rows: [(None, "nuclei", 1), (None, "cells", 1), (None, "cells", 2)]

Volumetric (C, Z, H, W) data is supported. The featurizer automatically skips 2D-only features (radial_distribution, radial_zernikes, zernike, feret). All other features (intensity, sizeshape, texture, granularity, correlations) work for both 2D and 3D.

The output is plain numpy + lists, so converting to a DataFrame is straightforward:

import pandas as pd
row_names = [f"{img}__{obj}__{label}" for img, obj, label in rows]
df = pd.DataFrame(data, index=row_names, columns=columns)

Note: DataFrame libraries must be installed independently, to keep the dependency tree low.

Important notes

• Contiguous labels: The input labels must be sequential (e.g., [1,2,3], not [1,3,4]). You can use skimage.segmentation.relabel_sequential to ensure compliance.
• Fidelity: If you need to match CellProfiler measurements 1:1, you must convert your image arrays to float values between 0 and 1. For instance, if you have an array of data type uint16, you must divide them all by 65535. This is important for radial distribution measurements.
• Speed: The Granularity measurement is particularly slow (~80% of the compute time). Skip this one it if speed is of utmost importance.

API Overview

For more control over individual measurements, or to call specific functions directly, use the bulk API. It operates on single images and masks following the scikit-image convention.

Details

cp_measure currently provides two types of measurements based on their inputs:

• Type 1: 1 image + 1 set of masks (e.g., intensity)
• Type 2: 2 images + 1 set of masks (e.g., colocalization)

import numpy as np
from cp_measure.bulk import get_core_measurements

measurements = get_core_measurements()
# print(measurements.keys())
# dict_keys(['radial_distribution', 'radial_zernikes', 'intensity', 'sizeshape', 'zernike', 'feret', 'texture', 'granularity'])

# Create synthetic data
size = 240
rng = np.random.default_rng(42)
pixels = rng.integers(low=1, high=255, size=(size, size))

# Create two similar-sized objects
masks = np.zeros_like(pixels)
masks[50:100, 50:100] = 1
masks[150:200, 150:200] = 2

measurements = get_core_measurements()
results = {}
for name, func in measurements.items():
    results = {**results, **func(masks, pixels)}

"""
{'RadialDistribution_FracAtD_1of4': array([0.03673493, 0.05640786]),
 'RadialDistribution_MeanFrac_1of4': array([1.02857809, 1.15072037]),
 'RadialDistribution_RadialCV_1of4': array([0.05539421, 0.04635982]),
 ...
 'Granularity_16': array([97.65759629, 97.64371833])
}
"""

Import a subset of measurements

Individual measurement functions can be imported directly. Each returns a dictionary of arrays.

import numpy as np
from cp_measure.core.measureobjectsizeshape import get_sizeshape

mask = np.zeros((50, 50), dtype=np.int32)
mask[5:-6, 5:-6] = 1
get_sizeshape(mask, None)

measureobjectintensitydistribution.get_radial_zernikes
measureobjectintensity.get_intensity
measureobjectsizeshape.get_zernike
measureobjectsizeshape.get_feret
measuregranularity.get_granularity
measuretexture.get_texture
measurecolocalization.get_correlation_pearson
measurecolocalization.get_correlation_manders_fold
measurecolocalization.get_correlation_rwc
measurecolocalization.get_correlation_costes
measurecolocalization.get_correlation_overlap

For Type 3 functions:

measureobjectoverlap.measureobjectoverlap
measureobjectneghbors.measureobjectneighboors

Similar projects

• spacr: Library to analyse screens, it provides measurements (independent implementation) and a GUI.
• ScaleFEX: Python pipeline that includes measurements, designed for the cloud.
• thyme: Rust library to extract a subset of CellProfiler's features efficiently (independent implementation).

Current work

You can follow progress here.

Most features are implemented, but Type 3 measurements (e.g., ObjectNeighbors) does not have a wrapper. We do not plan to implement ObjectSkeleton.

Contributing

See CONTRIBUTING.md for details.