Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

make deconvolution accept an optional psf and work in 3d #731

Open
sofroniewn opened this issue Oct 23, 2018 · 0 comments
Open

make deconvolution accept an optional psf and work in 3d #731

sofroniewn opened this issue Oct 23, 2018 · 0 comments
Labels
feature New work

Comments

@sofroniewn
Copy link
Collaborator

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

@sofroniewn sofroniewn added the feature New work label Oct 23, 2018
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
feature New work
Projects
None yet
Development

No branches or pull requests

1 participant