IlluminationCorrection#

The module provides a function to correct systematic illumination variations and vignetting in intensity.

The intensity image $I(x)$ given a flat field $F(x)$ and a background $B(x)$ the image is corrected to $C(x)$ as:

The module also has functionality to create flat field corections from measured intensity changes in a single direction, useful e.g. for lightsheet images, see e.g. flatfield_from_regression().

References

..[LSM] Fundamentals of Light Microscopy and Electronic Imaging, p. 421

correct_illumination(source, flatfield=None, background=None, scaling=None, dtype=None, verbose=False)[source]#

Correct illumination and background.

Arguments

sourcearray, str, or Source: The image to correct for illumination.
sinkarray, str, Source, or None: The sink to write results to.
flatfieldstr, array, Source or None: The flatfield estimate. If None, no flat field correction is done.
backgroundstr, array, Source or None: The background estimate. If None, background is assumed to be zero.
scalingfloat, ‘max’, ‘mean’ or None: Scale the corrected result by this factor. If ‘max’ or ‘mean’ scale the result to match the ‘max’ or ‘mean’. If None, don’t scale the result.
dtypedtype: Data type for output.
verbosebool: If true, print progress information.

Returns

correctedarray: Illumination corrected image.

Note

The intensity image $I(x)$ given a flat field $F(x)$ and a background $B(x)$ image is corrected to $C(x)$ as:

If the background is not given $B(x) = 0$ .

The correction is done slice by slice assuming the data was collected with a light sheet microscope.

The image is finally optionally scaled.

References

[1] Fundamentals of Light Microscopy and Electronic Imaging, p 421

See also

default_flatfield_line_file_name

flatfield_from_line(line, shape, axis=0, dtype=<class 'float'>)[source]#

Creates a 2d flat field image from a 1d line of estimated intensities.

Arguments

linearray: Array of intensities along the specified axis.
shapetuple: Shape of the resulting image.
axisint: Axis of the flat field line estimate.

Returns

flatfieldarray: Full 2d flat field.

flatfield_line_from_regression(source, sink=None, positions=None, method='polynomial', reverse=None, return_function=False, verbose=False)[source]#

Create flat field line fit from a list of positions and intensities.

Arguments

sourcestr, array or Source: Intensities as (n,)-vector or (n,m)-array of m intensity measurements at n points along an axis.
sinkstr, array, Source or None: Sink for the result.
positionsarray, ‘source’ or None: The positions of the soource points. If None, a linear increasing positions with equal spaccing is assumed. If ‘source’ take positions from first line of the source array.
method‘Gaussian’ or ‘Polynomial’: function type for the fit.
reversebool: Reverse the line fit after fitting.
return_functionbool: If True, also return the fitted function.
verbose :bool: Print and plot information for the fit.

Returns

fitarray: Fitted intensities on points.
fit_functionfunction: Fitted function.

Note

The fit is either to be assumed to be a ‘Gaussian’:

or follows a order 6 radial ‘Polynomial’

default_flat_field_line_file_name = '/home/crousseau/code/icm/ClearMap2-lf003/ClearMap/Resources/Microscope/lightsheet_flatfield_correction.csv'#

Default file of points along the illumination changing line for the flat field correction

See Also:: correct_illumination()