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
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 measure_gfp_fluorescence(fluorescent_image, worm_mask):
'''Given an image, measure the gfp flourescence
TODO: Do we need a worm_frame? Figure out how to add columns to the tsv files
'''
worm_pixels = fluorescent_image[worm_mask].copy()
#Get interesting statistics out
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 = np.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 = (fluorescent_image > expression_thresh) & worm_mask
high_expression_mask = (fluorescent_image >
high_expression_thresh) & worm_mask
#create dictionary to store the statistics/measurements
gfp_data = {
'warped_integrated_gfp': integrated,
'warped_median_gfp': median,
'warped_percentile95_gfp': percentile95,
'warped_expression_area_gfp': expression_area,
'warped_expression_areafraction_gfp': expression_area_fraction,
'warped_expression_mean_gfp': expression_mean,
'warped_high_expression_area_gfp': high_expression_area,
'warped_high_expression_area_fraction_gfp':
high_expression_area_fraction,
'warped_high_expression_mean_gfp': high_expression_mean,
'warped_high_expression_integrated_gfp': high_expression_integrated,
'warped_total_size': np.sum(worm_mask)
}
#Generate nice looking pictures to save
expression_area_mask = np.zeros(worm_mask.shape).astype('bool')
high_expression_area_mask = np.zeros(worm_mask.shape).astype('bool')
percentile95_mask = np.zeros(worm_mask.shape).astype('bool')
expression_area_mask[fluorescent_image > expression_thresh] = True
expression_area_mask[np.invert(worm_mask)] = False
high_expression_area_mask[
fluorescent_image > high_expression_thresh] = True
high_expression_area_mask[np.invert(worm_mask)] = False
percentile95_mask[fluorescent_image > percentile95] = True
percentile95_mask[np.invert(worm_mask)] = False
colored_areas = extractFeatures.color_features(
[expression_area_mask, high_expression_area_mask, percentile95_mask])
return (gfp_data, colored_areas)
def get_vignette_mask(image):
"""Convert a well-exposed image (ideally a brightfield image with ~uniform
intensity) into a mask delimiting the image region from the dark,
vignetted borders of the image.
Returns: vignette_mask, which is True in the image regions.
"""
likely_vignette_pixels = image[image < numpy.percentile(image, 40)]
mean, std = mcd.robust_mean_std(likely_vignette_pixels, 0.5)
vignette_threshold = mean + 150 * std
vignette_mask = image > vignette_threshold
vignette_mask = ndimage.binary_fill_holes(vignette_mask)
return vignette_mask
def subregion_measures(image, mask):
"""Measure region properties of a masked image, defining several sub-regions
relevant to fluorescence images.
Three sub-regions will be defined:
expression: the region of a fluorescence image where there is
apparent fluorescent protein expression (2.5 standard deviations
above the background distribution of low-valued pixels in the
masked region)
high_expression: the region of apparent intense fluorescence (6 standard
deviations above background)
over_99: the region including the top 1% of pixels by intensity.
Parameters:
image, mask: numpy.ndarrays of same shape.
Returns: data, region_masks
data:
[sum, mean, median, percentile_95, percentile_99,
expression_sum, expression_mean, expression_median,
expression_area_fraction,
high_expression_sum, high_expression_mean, high_expression_median,
high_expression_area_fraction,
over_99_sum, over_99_mean, over_99_median]
where the 'area_fraction' measurements represent the fraction of the
mask area encompassed by the expression and high_expression areas.
region_masks: [expression_mask, high_expression_mask, over_99_mask]
where each is a mask defining the sub-region of the mask.
"""
if mask.dtype != bool:
mask = mask > 0
pixels = image[mask]
mask_measures = region_measures(pixels)
mean = mask_measures[1]
area = pixels.sum()
low_mean, low_std = mcd.robust_mean_std(pixels[pixels < mean], 0.5)
expression_mask = (image > (low_mean + 2.5 * low_std)) & mask
expression_measures = region_measures(image[expression_mask])[:3]
expression_area_fraction = expression_mask.sum() / area
expression_measures.append(expression_area_fraction)
high_expression_mask = (image > (low_mean + 6 * low_std)) & mask
high_expression_measures = region_measures(image[high_expression_mask])[:3]
high_expression_area_fraction = high_expression_mask.sum() / area
high_expression_measures.append(high_expression_area_fraction)
percentile_99 = mask_measures[-1]
over_99_mask = (image > percentile_99) & mask
over_99_measures = region_measures(image[over_99_mask])[:3]
data = mask_measures + expression_measures + high_expression_measures + over_99_measures
region_masks = [expression_mask, high_expression_mask, over_99_mask]
return data, region_masks
def get_rough_mask(image):
"""Take an image with light wells and dark inter-well regions and construct
a mask with 'True' values in all pixels belonging to a well and 'False' values
elsewhere."""
# take every 3rd pixel in each direction and then flatten to a 1D array.
image_sample = image[::3, ::3].flatten()
# use that subsample to estimate the mean and variance of the background pixels
mean, std = mcd.robust_mean_std(image_sample, subset_fraction=0.5)
# find the non-background pixels
well_mask = image > (mean + 12*std)
well_mask = ndimage.binary_fill_holes(well_mask)
well_mask = mask.remove_small_radius_objects(well_mask, max_radius=10)
well_mask = mask.remove_edge_objects(well_mask)
return well_mask
def get_vignette_mask(image, percent_vignetted=5):
"""Convert a well-exposed image (ideally a brightfield image with ~uniform
intensity) into a mask delimiting the image region from the dark,
vignetted borders of the image.
percent_vignetted: percent (0-100) of pixels estimated to be in the vignetted region.
35% is a good estimate for images with a full circular vignette
(e.g. 0.7x optocoupler); 5% is reasonable for images with only small
vignetted areas (e.g. 1x optocoupler).
Returns: vignette_mask, which is True in the image regions.
"""
bright_pixels = image[image > numpy.percentile(image[::4,::4], 1.5*percent_vignetted)]
mean, std = mcd.robust_mean_std(bright_pixels[::10], 0.85)
vignette_threshold = mean - 5 * std
vignette_mask = image > vignette_threshold
vignette_mask = ndimage.binary_closing(vignette_mask)
vignette_mask = ndimage.binary_fill_holes(vignette_mask)
vignette_mask = ndimage.binary_opening(vignette_mask, iterations=15)
return vignette_mask
def get_vignette_mask(image, percent_vignetted=5):
"""Convert a well-exposed image (ideally a brightfield image with ~uniform
intensity) into a mask delimiting the image region from the dark,
vignetted borders of the image.
percent_vignetted: percent (0-100) of pixels estimated to be in the vignetted region.
35% is a good estimate for images with a full circular vignette
(e.g. 0.7x optocoupler); 5% is reasonable for images with only small
vignetted areas (e.g. 1x optocoupler).
Returns: vignette_mask, which is True in the image regions.
"""
bright_pixels = image[image > numpy.percentile(image[::4,::4], 1.5*percent_vignetted)]
mean, std = mcd.robust_mean_std(bright_pixels[::10], 0.85)
vignette_threshold = mean - 5 * std
vignette_mask = image > vignette_threshold
vignette_mask = ndimage.binary_closing(vignette_mask)
vignette_mask = ndimage.binary_fill_holes(vignette_mask)
vignette_mask = ndimage.binary_opening(vignette_mask, iterations=15)
return vignette_mask
def measure_gfp_fluorescence(fluorescent_image,
worm_mask,
measurement_name=None):
"""Measure specific GFP fluorescent things for a particular GFP image
and return a dictionary of the measurements
Parameters:
flourescent_image: numpy array of the flourescent image
worm_mask: numpy array of the mask
measurement_name: string of the descriptor that you want the columns to have
i.e. if you were measuring gfp in the head then you might put measurement_name = 'head'
and then in the output your dictionary will have keys such as 'integrated_gfp_head'
instead of 'integrated_gfp'. This makes it easier to input into elegant right away and
not overwrite any other previously made measurements
Returns:
gfp_measurements: dictionary of measurements and their values
NOTE: currently gfp_measurements has set things to look for, but maybe
in the future we can have this take functions to study.
"""
worm_pixels = fluorescent_image[worm_mask].copy()
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 = np.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 = (fluorescent_image > expression_thresh) & worm_mask
high_expression_mask = (fluorescent_image >
high_expression_thresh) & worm_mask
length = worm_mask.shape[0]
gfp_measurements = {
'integrated_gfp': integrated,
'median_gfp': median,
'percentile95_gfp': percentile95,
'expressionarea_gfp': expression_area,
'expressionareafraction_gfp': expression_area_fraction,
'expressionmean_gfp': expression_mean,
'highexpressionarea_gfp': high_expression_area,
'highexpressionareafraction_gfp': high_expression_area_fraction,
'highexpressionmean_gfp': high_expression_mean,
'highexpressionintegrated_gfp': high_expression_integrated,
'area': area,
'length': length
}
if measurement_name is not None:
for key in sorted(gfp_measurements.keys()):
gfp_measurements[key + "_" +
measurement_name] = gfp_measurements.pop(key)
expression_area_mask = np.zeros(worm_mask.shape).astype('bool')
high_expression_area_mask = np.zeros(worm_mask.shape).astype('bool')
percentile95_mask = np.zeros(worm_mask.shape).astype('bool')
expression_area_mask[fluorescent_image > expression_thresh] = True
expression_area_mask[np.invert(worm_mask)] = False
high_expression_area_mask[
fluorescent_image > high_expression_thresh] = True
high_expression_area_mask[np.invert(worm_mask)] = False
percentile95_mask[fluorescent_image > percentile95] = True
percentile95_mask[np.invert(worm_mask)] = False
#colored_areas = extractFeatures.color_features([expression_area_mask,high_expression_area_mask,percentile95_mask])
return gfp_measurements