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Polarimetry methods
Cristel Chandre edited this page Jul 1, 2024
·
24 revisions
![](https://github.com/cchandre/Polarimetry/raw/master/pypolar/icons/microscope.png)
- variables: (ρ, ψ).
- defined as: given
$I({\bf x},\alpha)=a_0({\bf x})+a_2({\bf x}) \cos 2\alpha +b_2({\bf x}) \sin 2\alpha$ where${\bf x}$ is the position of the pixel and$\alpha$ the polarization angle, the values of ρ and ψ are obtained using a linear interpolation on a pre-loaded disk cone. This disk cone can be changed in the Advanced option tab -
$\rho\in [0, 180^\circ[$ (orientation) and$\psi\in [0^\circ, 180^\circ]$ - reference: A. Kress, X. Wang, H. Ranchon, J. Savatier, H. Rigneault, P. Ferrand, S. Brasselet, Mapping the local organization of cell membranes using excitation-polarization-resolved confocal fluorescence microscopy, Biophys. J. 105, 127-136 (2013)
- variables: (ρ, S2, S4)
- defined as: given
$\sqrt{I({\bf x},\alpha)}=a_0({\bf x})+a_2({\bf x}) \cos 2\alpha +b_2({\bf x}) \sin 2\alpha + a_4({\bf x}) \cos 4\alpha +b_4({\bf x}) \sin 4\alpha$ where${\bf x}$ is the position of the pixel and$\alpha$ the polarization angle,$S_2({\bf x})=3\frac{\sqrt{a_2^2+b_2^2}}{2a_0}$ and$S_4({\bf x})=6\frac{\sqrt{a_4^2+b_4^2}}{a_0}\cos 4(\phi-\rho)$ where$\rho({\bf x})={\rm atan2} \frac{b_2}{a_2}$ and$\phi({\bf x})={\rm atan2} \frac{b_4}{a_4}$ -
$\rho\in [0, 180^\circ[$ (orientation),$S_2\in [0, 1]$ and$S_4\in [-1, 1]$ - reference: J. Duboisset, P. Berto, P. Gasecka, F.Z. Bioud, P. Ferrand, H. Rigneault, S. Brasselet, Molecular orientational order probed by coherent anti-Stokes Raman scattering (CARS) and stimulated Raman Scattering (SRS) microscopy: a spectral comparative study, J. Phys. Chem. B 119, 3242–3249 (2015)
- variables: (ρ, S2, S4)
- defined as: given
$I({\bf x},\alpha)=a_0({\bf x})+a_2({\bf x}) \cos 2\alpha +b_2({\bf x}) \sin 2\alpha + a_4({\bf x}) \cos 4\alpha +b_4({\bf x}) \sin 4\alpha$ where${\bf x}$ is the position of the pixel and$\alpha$ the polarization angle,$S_2({\bf x})=3\frac{\sqrt{a_2^2+b_2^2}}{2a_0}$ and$S_4({\bf x})=6\frac{\sqrt{a_4^2+b_4^2}}{a_0}\cos 4(\phi-\rho)$ where$\rho({\bf x})={\rm atan2} \frac{b_2}{a_2}$ and$\phi({\bf x})={\rm atan2} \frac{b_4}{a_4}$ -
$\rho\in [0, 180^\circ[$ (orientation),$S_2\in [0, 1]$ and$S_4\in [-1, 1]$ - reference: J. Duboisset, P. Berto, P. Gasecka, F.Z. Bioud, P. Ferrand, H. Rigneault, S. Brasselet, Molecular orientational order probed by coherent anti-Stokes Raman scattering (CARS) and stimulated Raman Scattering (SRS) microscopy: a spectral comparative study, J. Phys. Chem. B 119, 3242–3249 (2015)
- variables: (ρ, SSHG)
- defined as: given
$I({\bf x},\alpha)=a_0({\bf x})+a_2({\bf x}) \cos 2\alpha +b_2({\bf x}) \sin 2\alpha + a_4({\bf x}) \cos 4\alpha +b_4({\bf x}) \sin 4\alpha$ where${\bf x}$ is the position of the pixel and$\alpha$ the polarization angle,$S_{\rm SHG}({\bf x})=-\frac{\sqrt{a_4^2+b_4^2}-\sqrt{a_2^2+b_2^2}}{2\left(\sqrt{a_4^2+b_4^2}+\sqrt{a_2^2+b_2^2}\right)}-0.65$ and$\rho({\bf x})={\rm atan2} \frac{b_2}{a_2}$ -
$\rho\in [0, 180^\circ[$ (orientation) and$S_{\rm SHG}\in [-1, 1]$
- variables: (ρ, S2, S4)
- defined as in
SRS
- reference: P. Ferrand, P. Gasecka, A. Kress, X. Wang, F.Z. Bioud, J. Duboisset, S. Brasselet, Ultimate use of two-photon fluorescence microscopy to map orientational behavior of fluorophores. Biophys. J. 106 2330–2339 (2014)
- variables: (ρ, ψ)
-
$\rho\in [0, 180^\circ[$ (orientation) and$\psi\in [0^\circ, 180^\circ]$ - reference: C. Rimoli, C. Valades Cruz, V. Curcio, M. Mavrakis, S. Brasselet, 4polar-STORM polarized super-resolution imaging of actin filament organization in cells, Nat. Comm. 13, 301 (2022)
- variables: (ρ, ψ, η)
-
$\rho\in [0, 180^\circ[$ (orientation),$\psi\in [0^\circ, 180^\circ]$ and$\eta\in [0^\circ, 90^\circ]$
The colormap for ρ is hsv
(and colorwheel
from Colorcet for colorblind-friendly visualization).
The colormap for ψ, S2, S4, SSHG is jet
(and viridis
for colorblind-friendly visualization).
The colormap for η is plasma
.
PyPOLAR is developed under BSD 2-Clause License, Copyright(c) 2021 cristel.chandre@cnrs.fr