Implementing SURF-ref With MahotasΒΆ

This is a companion to the paper Determining the subcellular location of new proteins from microscope images using local features by Coelho et al. (2013).

def surf_ref(f, ref):
    features = surf_ref(f, ref)

    Computer SURF-ref features

    f : ndarray
        input image
    ref : ndarray
        Corresponding reference image

    features : ndarray
    fi = surf.integral(f.copy())
    points = surf.interest_points(fi, 6, 24, 1, max_points=1024, is_integral=True)
    descs = surf.descriptors(fi, points, is_integral=True, descriptor_only=True)
    if ref is None:
        return descs
    descsref = surf.descriptors(ref, points, descriptor_only=True)
    return np.hstack( (descs, descsref) )

This function can take any number of reference images.

We now compute all features for all images in widefield dataset:

from glob import glob
import re

basedir = 'rt-widefield' # Edit as needed

features = []
labels = []

# We need the following to keep track of the proteins:
origins = []
prev_origin = ''
origin_counter = -1 # set to -1 so it will be correctly initialized on the first image

for dir in glob(basedir):
    if dir == 'README': continue
    for f in glob('{}/{}/*-protein.tiff'.format(basedir, dir)):
        origin = f[:5]
        if origin != prev_origin:
            origin_counter += 1
            prev_origin = origin

        f = '{}/{}/{}'.format(basedir, dir, f)
        f = mh.imread(f)
        ref = mh.imread(f.replace('protein','dna'))
        features.append(surf_ref(f, ref))