Welcome to PartSeg measurement’s documentation!

PartSeg_measurement is extraction and generalization of the PartSeg measurement engine for napari imaging data.

Example of usage:

import numpy as np
import tifffile

from PartSeg_measurement import measurement, Image, Labels

@measurement
def volume(labels: Labels, voxel_size):
    """
    Calculate the volume of the object marked with positive pixels on labels array.
    """
    return np.count_nonzero(labels) * np.prod(voxel_size)

@measurement
def sum_of_pixel_brightness(labels: Labels, image: np.ndarray) -> float:
    """
    Calculate the sum of the pixel brightness of the object marked with positive pixels on labels array.
    """
    return np.sum(image[labels > 0]) if np.any(labels) else 0

density = sum_of_pixel_brightness / volume

image = tifffile.imread('image.tif')
labels = tifffile.imread('labels.tif')

print(f"Density: {density(labels=labels, image=image, voxel_size=(210, 70, 70))}")

Indices and tables