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OpenSMFS / FRETBursts

Burst analysis software for single and multi-spot single-molecule FRET (smFRET) data.
https://opensmfs.github.io/FRETBursts/
GNU General Public License v2.0
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Polarization Support #21

Open IronicFreedom opened 5 years ago

IronicFreedom commented 5 years ago

Is there already support for 4-channel nsALEX/PIE for anisotropy analysis? If not, is it planned to implement this in the near future?

tritemio commented 5 years ago

FRETBursts (from master) can load PIE 4-channel data from Photon-HDF5. The polarization information is stored in Data.S_em and Data.P_em. Like for Data.A_em and Data.D_em, these attributes are list of arrays in order to support multispot setups (for single-spot setup use Data.A_em[0] and so forth).

Burst search and selection can be performed as for 2-channel data using photons in both polarization.

Photons can then be sorted in the two polarization, but there is no specific function provided by FRETBursts, you need to use the arrays in Data.S_em and Data.P_em as masks and implement the fitting procedure to extract anisotropy.

I have no plan to add polarization support myself, but if somebody is motivated I would welcome and review a Pull Request. In this case, I would suggest to start implementing as much as possible as a notebook (see the other example notebooks) and later decide which functions to move to the FRETBursts library.