AreTomo to Warp reconstructions - work around for missing taSolutions.log odd/even tomogram reconstruction?

[R Nwo]

This might be a naive question but I am to try using cryoCARE for denoising my tomograms. I am using AreTomo for alignment/reconstruction of frame corrected images (originally processed using Warp). I then wanted to feed that alignment info back to Warp to reconstruct odd/even tomograms that could be used for training cryoCARE. However, AreTomo doesn't produce the taSolutions.log file required for the reconstruction in Warp. I was wondering if anyone has anyone had developed any workarounds for generating these odd/even tomos in Warp from data that wasn't aligned in IMOD?

[tom dendooven]

Hi R, 

Warp only needs the .xf files from Aretomo, it doesn't require the taSolutions.log file. 

I wrote a little Aretomo script that you can run in the imod folder in your Warp directory. It will run through your tilt series, align them with Aretomo and organise the required .xf files in a new folder, which you can then use for Warp.

https://gist.github.com/Dendooventom

Cheers,

Tom

On Wed, 5 Oct 2022 at 19:10, R Nwo <rnwo...@gmail.com> wrote:

This might be a naive question but I am to try using cryoCARE for denoising my tomograms. I am using AreTomo for alignment/reconstruction of frame corrected images (originally processed using Warp). I then wanted to feed that alignment info back to Warp to reconstruct odd/even tomograms that could be used for training cryoCARE. However, AreTomo doesn't produce the taSolutions.log file required for the reconstruction in Warp. I was wondering if anyone has anyone had developed any workarounds for generating these odd/even tomos in Warp from data that wasn't aligned in IMOD?

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[teg...@gmail.com]

Thank you, Tom, that is a very useful script! I think Lorenzo Gaifas is also working on harnessing the local alignments from AreTomo inside Warp.

Cheers,

Dimitry

[R Nwo]

This is very helpful! Thanks for sharing the script (and also the info about the taSolutions.log).

Best,

Robert

On Wednesday, October 5, 2022 at 11:35:43 AM UTC-7 tom.de...@gmail.com wrote: