PySMACKS

Overview

Python framework for single-molecule FRET data analysis. The general pipeline includes the following steps:

Modules that are ready for test:

Traces_extractor_pipeline.ipynb : JP notebook used to run the traces extraction from the raw TIFF movies, including chromatic aberration and drift corrections
PySMACKS_FRET_corrections.ipnyb : JP notebook used to process the FRET corrections $\alpha$ - $\delta$ - $\beta$ - $\gamma$, and plot the corrected FRET efficiency histogram
GUI_traces_viewer.py : A GUI traces viewer to manually check the extracted traces, filter them using SNR threshold and view the corresponding spot from the raw TIFF movies; will serve as a basis for the quality checks
GUI_traces_annotater.py : similar to GUI_traces_viewer.py, with additional function to select sub-regions of individual traces for downstream analysis, as well as some user-friendly feature, such as zooming with the mouse roll

Name		Name	Last commit message	Last commit date
Latest commit History 21 Commits
notebooks		notebooks
GUI_HMM_utils.py		GUI_HMM_utils.py
GUI_traces_annotater.py		GUI_traces_annotater.py
GUI_traces_viewer.py		GUI_traces_viewer.py
HMM_SMACKS_module.py		HMM_SMACKS_module.py
LICENSE.txt		LICENSE.txt
PySMACKS_GUI_PyQT5.py		PySMACKS_GUI_PyQT5.py
PySMACKS_GUI_PyQT5_SEhist.py		PySMACKS_GUI_PyQT5_SEhist.py
PySMACKS_GUI_PyQT5_extraction.py		PySMACKS_GUI_PyQT5_extraction.py
PySMACKS_GUI_PyQT5_filtering.py		PySMACKS_GUI_PyQT5_filtering.py
PySMACKS_GUI_PyQT5_kinetic.py		PySMACKS_GUI_PyQT5_kinetic.py
PySMACKS_GUI_PyQT5_registration.py		PySMACKS_GUI_PyQT5_registration.py
README.md		README.md
chromatic_aberrations_correction.py		chromatic_aberrations_correction.py
drift_correction.py		drift_correction.py
main.py		main.py
traces_extractor.py		traces_extractor.py
utils.py		utils.py