def overlay_cells_w_image(self, image):
"""Creates an overlay of the cells over the base image.
Besides the base image this method also requires the clipping
coordinates for the image"""
img = rgb2gray(img_as_float(image))
img = rescale_intensity(img)
return cp.overlay_cells(self.cells, img, self.cell_colors)
def overlay_cells_w_base(self, base_image, clip):
"""Creates an overlay of the cells over the base image.
Besides the base image this method also requires the clipping
coordinates for the image"""
x0, y0, x1, y1 = clip
base = color.rgb2gray(img_as_float(base_image[x0:x1, y0:y1]))
base = exposure.rescale_intensity(base)
self.base_w_cells = cp.overlay_cells(self.cells, base, self.cell_colors)
def overlay_cells_w_base(self, base_image, clip):
"""Creates an overlay of the cells over the base image.
Besides the base image this method also requires the clipping
coordinates for the image"""
x0, y0, x1, y1 = clip
base = color.rgb2gray(img_as_float(base_image[x0:x1, y0:y1]))
base = exposure.rescale_intensity(base)
self.base_w_cells = cp.overlay_cells(self.cells, base,
self.cell_colors)
def overlay_cells_w_optional(self, optional_image):
"""Creates an overlay of the cells over the optional image"""
optional = color.rgb2gray(img_as_float(optional_image))
optional = exposure.rescale_intensity(optional)
self.optional_w_cells = cp.overlay_cells(self.cells, optional,
self.cell_colors)
def overlay_cells_w_fluor(self, fluor_image):
"""Creates na overlay of the cells over the fluor image)"""
fluor = color.rgb2gray(img_as_float(fluor_image))
fluor = exposure.rescale_intensity(fluor)
self.fluor_w_cells = cp.overlay_cells(self.cells, fluor,
self.cell_colors)
def overlay_cells_w_fluor(self, fluor_image):
"""Creates na overlay of the cells over the fluor image)"""
fluor = color.rgb2gray(img_as_float(fluor_image))
fluor = exposure.rescale_intensity(fluor)
self.fluor_w_cells = cp.overlay_cells(self.cells, fluor, self.cell_colors)
