Bypassing to the 'direct' use of emClarity's template matching pipeline

Great job on the emClarity!

I am currently trying to use template matching pipeline of emClarity and not all, it would be useful to get your advice about the best way to achieve this, because I am hoping to bypass the emClarity steps like renaming tilt-series, tomograms, and linking of all files etc.

Currently, I do tilt-series alignment and reconstructions in IMOD (using weighted-back projection) and EMAN2 (Fourier-inversion). Therefore I have some of the following for each tilt-series.

(1) Motion-corrected stack (usually .st format) (2) Pre-transform file (.prexf) generated for coarse-alignment of the tilt-series stack. (3) Transform file (.xf file) generated from the patch-tracking model(4) Generally -4X binned whole tomogram (size is usually 1K by 1K by 300). (5) Many times, I trim and rotate the tomogram of (4) to remove the 'blank' voxels. Rotation, because I work with lamellae which have a substantial PreTilt. This rotation and trimming generates a much smaller tomogram than the one in (4) and is thus faster for template matching. I just have to 'readjust' the missing wedge information for the rotated and trimmed tomogram. (6) The usual set of files generated from IMOD's tilt-series alignment and reconstruction. (7) No 'local' alignment is done so, no local xf files. (8) For my other template matching pipeline, I have functions/wrapper that takes care of 'readying/managing' the template (e.g, resampling to match the pixel size of the tomogram) for template matching. I see that emClairty also has similar functions e.g. rescale.

What minimalistic set of functions/tools will allow me to do template-matching in emClarity, with the files I have?

Thanks

Digvijay

StochasticAnalytics / emClarity

Bypassing to the 'direct' use of emClarity's template matching pipeline #118