choosing parameters for Lightsheet microscopy data

[jesusdpa1]

Hi Eric,

I am planning on using flowdec to apply deconvolution for Lightsheet microscopy. I think you have the parameter extraction already integrated into cytokit with the experiment json file, but is there a way of doing the same thing directly with flowdec to apply for this type of images?

[eric-czech]

Certainly, there are several discussions in the issues on using this lib for lightsheet images specifically too (e.g. #12). The examples in the repo show lots of different ways to do it. This notebook shows arguments for the psf generator and 01_Lattice_Light_Sheet_Deconvolution.ipynb is a great tutorial. There is also a tutorial on deconvolving images too large for gpu memory using dask here.

[jesusdpa1]

Thanks!!