timzuntar / phoremic Goto Github PK

Explanations of practical uses for the code are lacking

Function handling in main.py needs to be streamlined. The current state can lead to confusion.

Q_eff is independent of photon energy for the time being.

Make sure the appropriate transforms (depletion beam defocusing, location relative to objective) are taken into account

Implement code to define simple band-pass filters without importing from a file.

The image simulation process is currently nearly equivalent to computing a PSF of the beam. To better illustrate the actual advantages of superresolution methods, a multi-pixel image of an area with non-uniform fluorophore distribution needs to be built up.

Implement a basic way to interface with the functions using Tkinter

Currently, the probability distribution used for generation of emitted photon wavelengths is adjusted by hand to fit the test spectrum "well enough". An automated solution is needed for two reasons: to avoid the necessity of manual adjustment for every fluorophore species and to optimize resource use. Since the code execution time is almost directly proportional to the number of sampling events, it is important that the distribution tracks the spectrum as closely as possible.

Two options are on the table:

• using predefined (most likely PyMC3) sampler functions at execution time or
• iteratively computing the most efficient function a priori and storing its parameters for future use

Include spectra of at least a few commonly used dyes.

Vibrational relaxation and triplet-singlet transition rates must currently be specified in the main file. Writing the values to a file like properties.dat and reading them from there would make more sense.

A function to calculate it exists, but it returns values that are wildly inconsistent with expected ones. Implementation is probably faulty.

As a stopgap, the cross-section can be manually entered as a variable.

STED_2D_intensity_normalization numerically integrates the more accurate intensity profile to determine a multiplicative factor. It's currently untested if the returned values make sense.

The generated plots don't include information about the sample or excitation light properties.

Identify suboptimal resource usage and try to improve it

The square sine function approximation is only valid for radii less than half a period. The function should return 0 for greater values.