Tutorial videos - StochasticAnalytics/emClarity GitHub Wiki
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Phase plate data
Data collected using a phase plate have only limited support in emClarity: * It is assumed that you moved to a new area for each tomogram * It is assumed that you have calculated the expected phase plate shift evolution over your data collection. E.g. for [TODO link ribo paper] the phase shift is predicted to start around 0.35*pi and end around 0.55*pi.
* Set PHASE_PLATE_SHIFT=[0.35,0.55]
* Set your defocus estimate and search range closely. I am not sure if overfocus conditions will be properly fit.
- This is currently broken - I'm just going to integrate CTF find as soon as I can. Sorry: /
- Overview on info related to emClarity (4:30)
- Coarse alignment with Imod/etomo (30:01)
- Initial CTF estimation (14:56)
- Select regions for reconstruction (8:21)
- Template matching - setup and run (9:35)
- Template matching - editing the results (13:14)
2d CTF correction (5:28)
- 2d corrected tilt-series exist only transiently and are generated automatically during 3d CTF correction. This program is fully deprecated.
- Initialize project, Average, Align (14:52)