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- calculate_dye_matrix(excitation_wavelengths, dyes, filter_wavelengths)
- Calculates the dye response matrix given the parameters used to image.
Parameters:
excitation_wavelengths: array like of integers, shape (channels,)
This specifies the wavelengths used to exite the dyes
dyes: array like of strings, shape (channels,)
This specifies which dyes are being used, the valid names are (case insensitive):
DAPI, G, T, A, C,
dye_responses: array like of numbers, shape (channels,)
The wavelengths
- color_correct(image, dye_matrix=None)
- Takes an image taken and estimates
the dye present by using the given dye response matrix.
This corrects for crosstalk between different channels
and dyes.
Params:
image : np.ndarray, shape (num_channels, width, height)
dye_matrix : np.ndarray, shape (num_dyes, num_channels)
if not provided this matrix is estimated by the function estimate_dye_matrix
Returns:
new_image : np.ndarray, shape (num_dyes, width, height)
- crosstalk_plot(image, corrected, dye_matrix, name='image')
- estimate_background(images, percent=5, gaussian=8)
- estimate_crosstalk(chan, chanref, percent=0.1, bins=8)
- Calculates the estimated crosstalk between the two channels,
returns the crosstalk from chanref to chan, or how much chan is dependant
on chanref.
- estimate_dye_matrix(image)
- Estimates the dye response matrix given an image.
This assumes that each dye corresponds to one channel,
and that the majority of the response to the dye is that
channel.
- illumination_correction(images, out=None, background=None)
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