search

hammerlab / flowdec

TensorFlow Deconvolution for Microscopy Data
Apache License 2.0
86 stars 26 forks source link

choosing parameters for Lightsheet microscopy data #30

Closed jesusdpa1 closed 4 years ago

jesusdpa1 commented 4 years ago

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 commented 4 years ago

Certainly, there are several discussions in the issues on using this lib for lightsheet images specifically too (e.g. https://github.com/hammerlab/flowdec/issues/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 commented 4 years ago

Thanks!!