Continue with collection while binning and reordering final stacks

[peteranmu]

Dear fabian,

Recently I tried collecting tilt-series using PACEtomo v1.8.1 targetPattern mode, and it's really great, fast and stable!

However, there was an efficiency concern. Currently, after completing a group of tilt-series, the binning and reordering of the stacks require a considerable amount of time, during which the data acquisition is suspended.

Is it possible that PACEtomo start the collection of the next group of tilt-series while simultaneously performing the binning and reordering for the previous group of stacks? I'm not sure whether SerialEM python scripts are allowed to do this.

Look forward to any insights you might have on this matter.

Best regards,
Peter Mu

[eisfabian]

Hi Peter,

Thank you so much! And thanks for reaching out!

I agree, the operations on the final stack can take quite a bit of time. Ideally, it would run in the background.
This is a bit difficult as PACEtomo is a single script right now and SerialEM will wait until this script is done before moving on to the next target. I would have to put the sorting in a separate script that can run outside SerialEM.
I will bump it up on my priority list and let you know once I figure something out!

Thanks again and best wishes,
Fabian

[eisfabian]

Hi Peter,

I finally finished implementing a way to call the tilt stack sorting in the background so PACEtomo can continue collecting in the meantime.
It does depend on some functions of SPACEtomo to work though so you will have to install the latest SPACEtomo version as well.
Here is the new PACEtomo script:
https://github.com/eisfabian/PACEtomo/blob/main/untested/PACEtomo.py
Please let me know if you get a chance to try it!

If it works well, I will implement the same for binning, etc.

Thanks again and best,
Fabian

[peteranmu]

Hi Fabian,

It's great to see the new implementation. I've read the code in the commit (although I'm not very familiar with this), and calling the tilt stack sorting in the background by SPACEtomo seems a good idea. 😄

We may have one-day Krios time next month, and I will try it then. (Hopefully the EM manager have updated SerialEM...)

Best regards,
Peter Mu