shape_detection#

Module with routines for shape and size detection of objects such as cells.

Note

The shape detection is based on a seeded and masked watershed. The module is based on the ndimage library. For faster implementation of intensity and radial measurements see the modules listed below.

detect_shape(source, seeds, threshold=None, verbose=False, processes=None)[source]#

Detect object shapes by generating a labeled image from seeds.

Arguments

sourcearray, str or Source: Source image.
seedsarray, str or Source: Cell centers as point coordinates.
thresholdfloat or None: Threshold to determine mask for watershed, pixel below this are treated as background. If None, the seeds are expanded indefinitely.
verbose :bool: If True, print progress info.

Returns

shapesarray: Labeled image, where each label indicates an object.

find_intensity(source, label, max_label=None, method='sum', verbose=False)[source]#

Find integrated intensity given object shapes as labeled image.

Arguments

sourcearray, str, or Source: Source to measure intensities from.
labelarray, str, or Source: Labeled image with a separate label for each object.
max_labelint or None: Maximal label to include. If None, use all.
method{‘sum’, ‘mean’, ‘max’, ‘min’}: Method to use to measure the intensities in each object’s area.
verbosebool: If True, print progress information.

Returns

intensitiesarray: Measured intensities.

find_size(label, max_label=None, verbose=False)[source]#

Find size given object shapes as a labled image

Arguments

labelarray, str or Source: Labeled image in which each object has its own label.
max_labelint or None: Maximal label to include, if None use all label.
verbosebool: Print progress info.

Returns

sizesarray: Measured intensities