Janssen Theory and Architecture Guides¶
This documentation provides comprehensive coverage of the physics and software architecture underlying janssen, a JAX-based framework for optical microscopy simulations and ptychographic reconstruction.
Target Audience¶
These guides are written for optics researchers who want to understand:
The mathematical foundations of coherent and partially coherent optics
How optical wavefronts propagate through the simulation pipeline
The physical meaning of simulation parameters and outputs
Guide Overview¶
Physics Foundations¶
Guide |
Description |
|---|---|
Spatial and temporal coherence, mode decomposition |
|
Fresnel, Fraunhofer, and Angular Spectrum methods |
|
Phase retrieval algorithms (ePIE, gradient-based) |
|
Optical aberrations and wavefront decomposition |
|
High-NA focusing with Richards-Wolf integrals |
Architecture¶
Guide |
Description |
|---|---|
JAX data structures for GPU acceleration |
|
Common pitfalls and how to avoid them |
Mathematical Notation¶
Throughout these guides, we use:
$\lambda$ for wavelength (in meters)
$k = 2\pi/\lambda$ for wavenumber
$\mathbf{E}$ for electric field
$I = |\mathbf{E}|^2$ for intensity
$\phi$ for phase