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, backgorund 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, dont scale the result.

processesint or None

Number of processes to use. If None use macimal available.

verbosebool

If true, print progrss infomration.

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/ckirst/Programs/ClearMap2/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()