cylindra

Highlights

• Use acryo for subtomogram averaging. Accordingly, many simplification and improvements in structural reconstruction.
• Experimental polarity check functions.
• Viterbi alignment of distance-constrained and distance-and-angle-constrained method (implemented in C++).
• Missing wedge compensation.
• Curvature-oriented approximation of 3D spline. Accordingly, global variable is changed to fit this.

New Features

• Use relative path in project file if possible.
• Add binning option in local/global-CFT.
• Use Yen's thresholding to determine proper iso-surface threshold to show reconstruction.
• Write time spent on each long-running algorithm in log.
• Support "nearest" interpolation.
• Add method in GUI to concatenate molecule layers.

Changes

• Change in default arguments (interpolation of subtomogram alignment: 1 → 3; alignment method: PCC → ZNCC).

Seems very stable now.

New Features

• Molecules rendering.
• Both PCC and ZNCC are working.
• Use magic-class's thread_worker instead of napari built-in. Concomitantly, remove nbatch arguments.
• Add previews to some methods.
• Multi-template alignment worked.
• align_averaged tries many rotation angles than before.
• Add translate_random to Molecules.
• Improved convolution of molecule intervals.

Designs

• Capitalization using set_design to follow Python naming rules.
• Alignment is largely refactored.
• Port features to Molecules.
• Merge feature control and feature viewer into a single widget.

Bug Fixes

• Fix min/max of skew angle. Verified using TMV images.

• Add image processor and image previewer.
• Use ZNCC instead of PCC for spline fitting and refinement.
• Fix layers.events.removing.

GUI is largely improved.

• Subtomogram averaging
• Molecule feature visualization
• Project management
• More comprehensive tests

• Algorithms of fitting, monomer mapping seem almost stable.
• Molecules works without any fatal bugs.
• Good compatibility with PEET.

Bug Fixes

• Coordinate transformation was not correct! Now both Cartesian, cylindric coordinate transformation returns correct images.
• Tomogram list double-click callback used to load wrong results.

New Features

• Macro can be executed in console (don't start worker when function is called outside the GUI).
• New spline refinement algorithm fit_mao.

Changes

• Faster (~2x) iterative phase cross correlation using ft_pcc_maximum in impy==1.24.2.
• Faster (~2x) phase cross correlation with mirrored image by calculating FT image mathematically.
• Simpler API in some functions.
• Renamed.
  • paths → splines
  • n_paths → n_splines
  • ft_params → local_ft_params

Basic algorithms seem stable and perform very well.

• fit → OK
• refine → OK
• measure_radius → OK
• ft_params → OK
• global_ft_params → sometimes fails due to bug in straightening.

GUI needs more improvement, but this might be done in the magic-class side.

Last update with current algorithm design.
There would be a big change after this version but basically its performance should not change.

Basic functions are working well.
Many of them are dependent on impy.