PACE-tomo workflow

[asarnow]

First, let me say thank you, PYP is awesome and IMO is game changing for the cryo-ET software landscape.

I was wondering if there is an existing workflow for parallel tilt series data from PACE-tomo?

My files from PACE-tomo don't quite match the TILTSERIES_SCANORD_ANGLE pattern, because each parallel tilt series is interleaved in SCANORD, with a shared TILTSERIES (or really, "TARGET") label. For example with 41 tilts and 5 parallel tilt series, the SCANORD goes from 1 to 205, with e.g. 1, 42, 83, etc. identifying the first image in each series. They are always completely uniform, so splitting them modulo the number of tilts is reliable/easy. There are also .mdoc files for each TS, but I am not sure how to use these with PYP. There's no place to specify a directory for .mdoc files and placing them alongside the movies doesn't seem to work.

[abartesaghi]

Thanks @asarnow, you are right, the current version of nextPYP will not read these PACE-tomo .mdoc files because the tilt-series names do not match the name of the frames. This is a simple change though, so we will include this functionality in the next maintenance version of nextPYP which is scheduled to be released in the next couple of days.

[abartesaghi]

This feature has been implemented in v0.5.1. All frames and mdoc files should be placed in the same folder and the option Read metadata from mdoc files should be checked (Frame alignment tab, Pre-processing block).