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the current deconvolution exposed to the user only accepts sigma values and generates a gaussian psf to pass to the richardson-lucy deconvolution from skimage. Instead there are times when the user may have a custom psf, represented as an array of the same dimensions of the image. Users should be able to path both a custom psf and a sigma as inputs.
Also the current sigma is used to create a 2D psf automatically, but instead a psf the dimensions of the input array should be created, as the richardson-lucy deconvolution from skimage works in ND. Finally a list of sigma values of the same length as the number of dimensions should also be passable as an input argument and an anisotropic gaussian should be generated accordingly. This is particulalry useful for volumetric imaging which is often anisotropic.
Finally deconvolution can often introduce some nasty artifacts at the boundaries of the image (related to the size of the psf) that can trip up spot detection further down the line (spurious local maxima are introduced). We might want the option to zero the boundary region too
The text was updated successfully, but these errors were encountered:
the current deconvolution exposed to the user only accepts sigma values and generates a gaussian psf to pass to the
richardson-lucy
deconvolution fromskimage
. Instead there are times when the user may have a custom psf, represented as an array of the same dimensions of the image. Users should be able to path both a custom psf and a sigma as inputs.Also the current sigma is used to create a 2D psf automatically, but instead a psf the dimensions of the input array should be created, as the
richardson-lucy
deconvolution fromskimage
works in ND. Finally a list of sigma values of the same length as the number of dimensions should also be passable as an input argument and an anisotropic gaussian should be generated accordingly. This is particulalry useful for volumetric imaging which is often anisotropic.Finally deconvolution can often introduce some nasty artifacts at the boundaries of the image (related to the size of the psf) that can trip up spot detection further down the line (spurious local maxima are introduced). We might want the option to
zero
the boundary region tooThe text was updated successfully, but these errors were encountered: