ShapeDetection

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.

See also

ClearMap.Analysis.Measurements.MeasureExpression, ClearMap.Analysis.Measurements.MeasureRadius

detect_shape(source, seeds, threshold=None, verbose=False)

Detect object shapes by generatng 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 indefinately.

verbose :bool

If True, print progress info.

Returns

shapesarray

Labeled image, where each label indicates a object.

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

Find integrated intensity given object shapes as labled 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)

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