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preprocessing.rst

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Image preparation

bigfish.stack

Functions used to normalize, format, cast, project or filter images.

Normalize images

Rescale or contrast pixel intensity:

  • bigfish.stack.rescale
  • bigfish.stack.compute_image_standardization

rescale

compute_image_standardization

Format images

Resize and pad images:

  • bigfish.stack.resize_image
  • bigfish.stack.get_marge_padding

resize_image

get_marge_padding

Cast images

Cast images to a specified dtype (with respect to the image range of values):

  • bigfish.stack.cast_img_uint8
  • bigfish.stack.cast_img_uint16
  • bigfish.stack.cast_img_float32
  • bigfish.stack.cast_img_float64

cast_img_uint8

cast_img_uint16

cast_img_float32

cast_img_float64

Filter images

Apply filtering transformations:

  • bigfish.stack.mean_filter
  • bigfish.stack.median_filter
  • bigfish.stack.gaussian_filter
  • bigfish.stack.maximum_filter
  • bigfish.stack.minimum_filter
  • bigfish.stack.dilation_filter
  • bigfish.stack.erosion_filter

Use Laplacian of Gaussian (LoG) filter to enhance peak signals and denoise the rest of the image:

  • bigfish.stack.log_filter

Use blurring filters with large kernel to estimate and remove background signal:

  • bigfish.stack.remove_background_mean
  • bigfish.stack.remove_background_gaussian

mean_filter

median_filter

gaussian_filter

maximum_filter

minimum_filter

dilation_filter

erosion_filter

log_filter

remove_background_mean

remove_background_gaussian

Project images in 2D

Build a 2D projection by computing the maximum, mean or median values:

  • bigfish.stack.maximum_projection
  • bigfish.stack.mean_projection
  • bigfish.stack.median_projection

maximum_projection

mean_projection

median_projection

Clean out-of-focus pixels

Compute a pixel-wise focus score:

  • bigfish.stack.compute_focus

Remove the out-of-focus z-slices of a 3D image:

  • bigfish.stack.in_focus_selection
  • bigfish.stack.get_in_focus_indices

Build a 2D projection by removing the out-of-focus z-slices/pixels:

  • bigfish.stack.focus_projection

compute_focus

in_focus_selection

get_in_focus_indices

focus_projection