def measure_fluorescence(image, worm_mask, well_mask=None):
if well_mask is not None:
restricted_mask = ndimage.binary_erosion(well_mask, iterations=15)
background = polyfit.fit_polynomial(image[::4,::4], mask=restricted_mask[::4,::4], degree=2).astype(numpy.float32)
background = ndimage.zoom(background, 4)
background /= background[well_mask].mean()
background[background <= 0.01] = 1 # we're going to divide by background, so prevent div/0 errors
image = image.astype(numpy.float32) / background
image[~well_mask] = 0
worm_pixels = image[worm_mask]
low_px_mean, low_px_std = mcd.robust_mean_std(worm_pixels[worm_pixels < worm_pixels.mean()], 0.5)
expression_thresh = low_px_mean + 2.5*low_px_std
high_expression_thresh = low_px_mean + 6*low_px_std
fluo_px = worm_pixels[worm_pixels > expression_thresh]
high_fluo_px = worm_pixels[worm_pixels > high_expression_thresh]
area = worm_mask.sum()
integrated = worm_pixels.sum()
median, percentile95 = numpy.percentile(worm_pixels, [50, 95])
expression_area = fluo_px.size
expression_area_fraction = expression_area / area
expression_mean = fluo_px.mean()
high_expression_area = high_fluo_px.size
high_expression_area_fraction = high_expression_area / area
high_expression_mean = high_fluo_px.mean()
high_expression_integrated = high_fluo_px.sum()
expression_mask = (image > expression_thresh) & worm_mask
high_expression_mask = (image > high_expression_thresh) & worm_mask
return data_row(area, integrated, median, percentile95,
expression_area, expression_area_fraction, expression_mean,
high_expression_area, high_expression_area_fraction,
high_expression_mean, high_expression_integrated), (image, background, expression_mask, high_expression_mask)
def refine_worm(image, initial_area, candidate_edges):
# find strong worm edges (roughly equivalent to the edges found by find_initial_worm,
# which are in candidate_edges): smooth the image, do canny edge-finding, and
# then keep only those edges near candidate_edges
smooth_image = restoration.denoise_tv_bregman(image, 140).astype(numpy.float32)
smoothed, gradient, sobel = canny.prepare_canny(smooth_image, 8, initial_area)
local_maxima = canny.canny_local_maxima(gradient, sobel)
candidate_edge_region = ndimage.binary_dilation(candidate_edges, iterations=4)
strong_edges = local_maxima & candidate_edge_region
# Now threshold the image to find dark blobs as our initial worm region
# First, find areas in the initial region unlikely to be worm pixels
mean, std = mcd.robust_mean_std(smooth_image[initial_area][::4], 0.85)
non_worm = (smooth_image > mean - std) & initial_area
# now fit a smoothly varying polynomial to the non-worm pixels in the initial
# region of interest, and subtract that from the actual image to generate
# an image with a flat illumination field
background = polyfit.fit_polynomial(smooth_image, mask=non_worm, degree=2)
minus_bg = smooth_image - background
# now recalculate a threshold from the background-subtracted pixels
mean, std = mcd.robust_mean_std(minus_bg[initial_area][::4], 0.85)
initial_worm = (minus_bg < mean - std) & initial_area
# Add any pixels near the strong edges to our candidate worm position
initial_worm |= ndimage.binary_dilation(strong_edges, iterations=3)
initial_worm = mask.fill_small_radius_holes(initial_worm, 5)
# Now grow/shrink the initial_worm region so that as many of the strong
# edges from the canny filter are in contact with the region edges as possible.
ac = active_contour.EdgeClaimingAdvection(initial_worm, strong_edges,
max_region_mask=initial_area)
stopper = active_contour.StoppingCondition(ac, max_iterations=100)
while stopper.should_continue():
ac.advect(iters=1)
ac.smooth(iters=1, depth=2)
worm_mask = mask.fill_small_radius_holes(ac.mask, 7)
# Now, get edges from the image at a finer scale
smoothed, gradient, sobel = canny.prepare_canny(smooth_image, 0.3, initial_area)
local_maxima = canny.canny_local_maxima(gradient, sobel)
strong_sum = strong_edges.sum()
highp = 100 * (1 - 1.5*strong_sum/local_maxima.sum())
lowp = max(100 * (1 - 3*strong_sum/local_maxima.sum()), 0)
low_worm, high_worm = numpy.percentile(gradient[local_maxima], [lowp, highp])
fine_edges = canny.canny_hysteresis(local_maxima, gradient, low_worm, high_worm)
# Expand out the identified worm area to include any of these finer edges
closed_edges = ndimage.binary_closing(fine_edges, structure=S)
worm = ndimage.binary_propagation(worm_mask, mask=worm_mask|closed_edges, structure=S)
worm = ndimage.binary_closing(worm, structure=S, iterations=2)
worm = mask.fill_small_radius_holes(worm, 5)
worm = ndimage.binary_opening(worm)
worm = mask.get_largest_object(worm)
# Last, smooth the shape a bit to reduce sharp corners, but not too much to
# sand off the tail
ac = active_contour.CurvatureMorphology(worm, max_region_mask=initial_area)
ac.smooth(depth=2, iters=2)
return strong_edges, ac.mask