jicbioimage.transform

Module containing image transformation functions.

The jicbioimage.transform module contains a number of built-in general purpose transformations that have had the jicbioimage.core.transformation() function decorator applied to them.

jicbioimage.transform.dilate_binary(*args, **kwargs)[source]

Return dilated image.

Parameters:
  • image – jicbioimage.core.image.Image
  • selem – neighborhood expressed as 1’s and 0’s, default is a cross
Returns:

dilated image
jicbioimage.transform.erode_binary(*args, **kwargs)[source]

Return eroded image.

Parameters:
  • image – jicbioimage.core.image.Image
  • selem – neighborhood expressed as 1’s and 0’s, default is a cross
Returns:

eroded image
jicbioimage.transform.find_edges_sobel(*args, **kwargs)[source]

Return edges detected using the Sobel method.

Parameters:
  • image – jicbioimage.core.image.Image
  • mask – Optional mask indicating regions to ignore
Returns:

eroded image
jicbioimage.transform.invert(*args, **kwargs)[source]

Return an inverted image of the same dtype.

Assumes the full range of the input dtype is in use and that no negative values are present in the input image.

Parameters:image – jicbioimage.core.image.Image
Returns:inverted image of the same dtype as the input
jicbioimage.transform.max_intensity_projection(*args, **kwargs)[source]

Return maximum intensity projection of a stack.

Parameters:stack – 3D array from which to project third dimension
Returns:jicbioimage.core.image.Image
jicbioimage.transform.mean_intensity_projection(*args, **kwargs)[source]

Return mean intensity projection of a stack.

Parameters:stack – 3D array from which to project third dimension
Returns:jicbioimage.core.image.Image
jicbioimage.transform.median_intensity_projection(*args, **kwargs)[source]

Return mean intensity projection of a stack.

Parameters:stack – 3D array from which to project third dimension
Returns:jicbioimage.core.image.Image
jicbioimage.transform.min_intensity_projection(*args, **kwargs)[source]

Return minimum intensity projection of a stack.

Parameters:stack – 3D array from which to project third dimension
Returns:jicbioimage.core.image.Image
jicbioimage.transform.remove_small_objects(*args, **kwargs)[source]

Remove small objects from an boolean image.

Parameters:image – boolean numpy array or jicbioimage.core.image.Image
Returns:boolean jicbioimage.core.image.Image
jicbioimage.transform.smooth_gaussian(*args, **kwargs)[source]

Returns Gaussian smoothed image.

Parameters:
  • image – numpy array or jicbioimage.core.image.Image
  • sigma – standard deviation
Returns:

jicbioimage.core.image.Image
jicbioimage.transform.threshold_otsu(*args, **kwargs)[source]

Return image thresholded using Otsu’s method.