LightsheetCorrection#
Module to remove lightsheet artifacts in images.
- correct_lightsheet(source, percentile=0.25, max_bin=4096, mask=None, lightsheet={'selem': (150, 1, 1)}, background={'dtype': <class 'float'>, 'interpolate': 1, 'selem': (200, 200, 1), 'spacing': (25, 25, 1), 'step': (2, 2, 1)}, lightsheet_vs_background=2, return_lightsheet=False, return_background=False, verbose=False)[source]#
Removes lightsheet artifacts.
Arguments
- sourcearray
The source to correct.
- percentilefloat in [0,1]
The percentile to base the lightsheet correction on.
- max_binint
The maximal bin to use. Max_bin needs to be >= the maximal value in the source.
- maskarray or None
Optional mask.
- lightsheetdict
Parameter to pass to the percentile routine for the lightsheet artifact estimate. See
ImageProcessing.Filter.Rank.percentile().- backgrounddict
Parameter to pass to the percentile routine for the background estimation.
- lightsheet_vs_backgroundfloat
The background is multiplied by this weight before comparing to the lightsheet artifact estimate.
- return_lightsheetbool
If True, return the lightsheet artifact estimate.
- return_backgroundbool
If True, return the background estimate.
- verbosebool
If True, print progress information.
Returns
- correctedarray
Lightsheet artifact corrected image.
- lightsheetarray
The lightsheet artifact estimate.
- backgroundarray
The background estimate.
Note
The routine implements a fast but effective way to remove lightsheet artifacts. Effectively the percentile in an eloganted structural element along the lightsheet direction centered around each pixel is calculated and then compared to the percentile in a symmetrical box like structural element at the same pixel. The former is an estimate of the lightsheet artifact the latter of the background. The background is multiplied by the factor lightsheet_vs_background and then the minimum of both results is subtracted from the source. Adding an overall background estimate helps to not accidentally remove vessel like structures along the light-sheet direction.
- correct_lightsheet_divide(source, percentile=0.25, max_bin=4096, mask=None, lightsheet={'selem': (150, 1, 1)}, background={'dtype': <class 'float'>, 'interpolate': 1, 'selem': (200, 200, 1), 'spacing': (25, 25, 1), 'step': (2, 2, 1)}, lightsheet_minimum=1, lightsheet_maximum=None, return_lightsheet=False, return_background=False, verbose=False)[source]#
Removes lightsheet artifacts.
Arguments
- sourcearray
The source to correct.
- percentilefloat in [0,1]
The percentile to base the lightsheet correction on.
- max_binint
The maximal bin to use. Max_bin needs to be >= the maximal value in the source.
- maskarray or None
Optional mask.
- lightsheetdict
Parameter to pass to the percentile routine for the lightsheet artifact estimate. See
ImageProcessing.Filter.Rank.percentile().- backgrounddict
Parameter to pass to the percentile routine for the background estimation.
- lightsheet_vs_backgroundfloat
The background is multiplied by this weight before comparing to the lightsheet artifact estimate.
- return_lightsheetbool
If True, return the lightsheet artifact estimate.
- return_backgroundbool
If True, return the background estimate.
- verbosebool
If True, print progress information.
Returns
- correctedarray
Lightsheet artifact corrected image.
- lightsheetarray
The lightsheet artifact estimate.
- backgroundarray
The background estimate.
Note
The routine implements a fast but effective way to remove lightsheet artifacts. Effectively the percentile in an eloganted structural element along the lightsheet direction centered around each pixel is calculated and then compared to the percentile in a symmetrical box like structural element at the same pixel. The former is an estimate of the lightsheet artifact the latter of the background. The background is multiplied by the factor lightsheet_vs_background and then the minimum of both results is subtracted from the source. Adding an overall background estimate helps to not accidentally remove vessel like structures along the light-sheet direction.
- correct_lightsheet_subdiv(source, percentile=0.25, max_bin=4096, mask=None, lightsheet={'selem': (150, 1, 1)}, background={'dtype': <class 'float'>, 'interpolate': 1, 'selem': (200, 200, 1), 'spacing': (25, 25, 1), 'step': (2, 2, 1)}, lightsheet_minimum=1, lightsheet_maximum=None, return_lightsheet=False, return_background=False, verbose=False)[source]#
Removes lightsheet artifacts.
Arguments
- sourcearray
The source to correct.
- percentilefloat in [0,1]
The percentile to base the lightsheet correction on.
- max_binint
The maximal bin to use. Max_bin needs to be >= the maximal value in the source.
- maskarray or None
Optional mask.
- lightsheetdict
Parameter to pass to the percentile routine for the lightsheet artifact estimate. See
ImageProcessing.Filter.Rank.percentile().- backgrounddict
Parameter to pass to the percentile routine for the background estimation.
- lightsheet_vs_backgroundfloat
The background is multiplied by this weight before comparing to the lightsheet artifact estimate.
- return_lightsheetbool
If True, return the lightsheet artifact estimate.
- return_backgroundbool
If True, return the background estimate.
- verbosebool
If True, print progress information.
Returns
- correctedarray
Lightsheet artifact corrected image.
- lightsheetarray
The lightsheet artifact estimate.
- backgroundarray
The background estimate.
Note
The routine implements a fast but effective way to remove lightsheet artifacts. Effectively the percentile in an eloganted structural element along the lightsheet direction centered around each pixel is calculated and then compared to the percentile in a symmetrical box like structural element at the same pixel. The former is an estimate of the lightsheet artifact the latter of the background. The background is multiplied by the factor lightsheet_vs_background and then the minimum of both results is subtracted from the source. Adding an overall background estimate helps to not accidentally remove vessel like structures along the light-sheet direction.