User story
As a user
I want to be able to pre-process my smFRET traces using the Papylio Python library
And to perform the HMM states calling using PySMACKS
So I can get the best from the two libraries
Additional information
The Papylio library by the Joo Lab (see study 10.1038/s41596-025-01196-y) seems to be optimized for smFRET analysis starting from the raw movies, and it is a Python library. Their HMM states caller is currently only able to work with a two state model and single variable (see here).
Once the PySMACKS HMM caller is ready, I suggest to work with the Papylio dev team to integrate PySMACKS into Papylio, so this framework benefits from the SMACKS advanced tools and we benefit from the Papylio already existing features.
User story
Additional information
The Papylio library by the Joo Lab (see study 10.1038/s41596-025-01196-y) seems to be optimized for smFRET analysis starting from the raw movies, and it is a Python library. Their HMM states caller is currently only able to work with a two state model and single variable (see here).
Once the PySMACKS HMM caller is ready, I suggest to work with the Papylio dev team to integrate PySMACKS into Papylio, so this framework benefits from the SMACKS advanced tools and we benefit from the Papylio already existing features.