Open talonchandler opened 1 year ago
@talonchandler Here is my reading of inputs and outputs, and suggestions for naming conventions:
2D -> isotropic_fluorescent_thin_3d
: 3D input is a short z-stack (say 5 slices covering the DOF) and output is the restored fluorescence at the plane of focus using defocused OTFs. Analogous to isotropic_phase_thin_3D
.
3D -> isotropic_fluorescent_thick_3d
: 3D deconvolution.
We should also add isotropic_fluorescent_thin_2D
, which would be a simple 2D deconvolution with 2D OTF.
The most basic (geometric) model for fluorescence anisotropy Fluor_anisotropy_recon
may be named inplane_orientation_fluorescent_thick_pol3d
. The input is a 3D polarization-resolved stack and the output are 3D as well. I am suggesting orientation
over the word fluorescence anisotropy because anisotropy signifies rotational diffusion to many.
Yes, isotropic_fluorescent_thick_3d
is immediately useful - please prioritize that while keeping in mind the overall dependencies between different models.
Great, I like these suggestions a lot.
isotropic_fluorescent_thick_3d
is the highest priority, and the following three can follow later:
isotropic_fluorescent_thin_3d
isotropic_fluorescent_thin_2d
inplane_oriented_fluorescent_thick_pol3d
The highest-priority fluorescence reconstruction isotropic_fluorescent_thick_3d
was migrated to torch
in #128.
I'm collecting the remaining migrations into a list here:
isotropic_fluorescent_thin_3d
isotropic_fluorescent_thin_2d
inplane_oriented_fluorescent_thick_pol3d
I'm planning to move the fluorescence reconstructions to
torch
and to the newmodel
-based structure.waveorder_reconstructor/fluorescence_microscopy
class will eventually be deprecatedfluorescence_microscopy
class supports2D
,3D
, andfluorescence anisotropy
reconstructions. Following our<sample_type>_<sample_thickness>_<data_type>
model-name schema, I will suggest moving+renaming these reconstructions to:2D
->isotropic_fluorescent_thin_3d
3D
->isotropic_fluorescent_thick_3d
fluorescence anisotropy
->inplane_anisotropic_fluorescent_thin_pol3d
@mattersoflight naming discussion is welcome.
@mattersoflight @edyoshikun if our immediate needs require just the
isotropic_fluorescent_thick_3d
, then I will prioritize that model.