Is dose weighting performed on tiltseries in WarpTools?

[Maurice Frijns]

Hi all,

I couldn't find anywhere in the documentation of WarpTools if dose weighting is performed during motion correction for tilt series, I assume not as the required input is not provided. Is that a correct assumption? and if so, is dose weighting performed during a later step?

Cheers,

Maurice 

[Alister Burt]

Hi Maurice,

Dose weighting is applied during movie export based on the per-frame dose supplied in your input settings file

https://github.com/warpem/warp/blob/656a2d4ff1ed9ab9ecbd6b5cf9d27db8c134284a/WarpLib/Movie/Movie.ExportMovie.cs#L202-L206

Dose weighting is also applied when reconstructing particle series for export to RELION

https://github.com/warpem/warp/blob/656a2d4ff1ed9ab9ecbd6b5cf9d27db8c134284a/WarpLib/TiltSeries/TiltSeries.ReconstructParticleSeries.cs#L114-L140

I remember Dimitry saying that the effects of dose weighting being applied twice, first to the movie and then cumulatively at the tilt series level, were accounted for - I assume this is true but couldn't find it quickly poking around the code, it's probably done in M somewhere :-)

Cheers,

Alister

--
You received this message because you are subscribed to the Google Groups "Warp" group.
To unsubscribe from this group and stop receiving emails from it, send an email to warp-em+u...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/warp-em/e909d149-3468-4213-9e5f-6f45113f3a84n%40googlegroups.com.

[Pranav Shah]

Isn’t it the case that during ts preprocessing,   no dose-weighting is applied to the 0-tilt image? (See the tomostar file - the 0 tilt will be listed as having 0 cumulative dose)

Best,
Pranav
--
Pranav Shah
Postdoctoral Research Fellow.

Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive, Oxford OX3 7BN,
UK

To view this discussion visit https://groups.google.com/d/msgid/warp-em/CAOt3kHqpzApTPNc1Rs00veJEv3MhP%3DrK2btKr4Y-0SZNpO3Nyg%40mail.gmail.com.

[Maurice Frijns]

Hi Allister,

Thanks for the quick reply, very helpful!

I’m still fairly new to tomography processing, so I just wanted to clarify something. I was under the impression that template matching generally gives better results when performed on dose-weighted tomograms.

If dose weighting of the tilt series is only applied in M, does that mean I’d be running template matching on non–dose-weighted tomograms when using WarpTools-preprocessed data?

Thanks again for your help!

Cheers, 

Maurice

Op zondag 12 oktober 2025 om 22:58:52 UTC+2 schreef alist...@gmail.com:

[Alister Burt]

Hi Maurice,

Good question! Your statement is a bit simplistic - doing TM well relies on knowing exactly what was done to the data prior to and during reconstruction. Warp knows exactly what it did and accounts for all of that internally, there are some good notes in the Warp paper.

What other TM implementations require as input to perform optimally is basically the wild west...

Recommended reading if interested: https://pubmed.ncbi.nlm.nih.gov/15065679/

Cheers,

Alister

To view this discussion visit https://groups.google.com/d/msgid/warp-em/256cfc94-b92a-4ade-bdf1-20739bc603dfn%40googlegroups.com.

[teg...@gmail.com]

Dose weighting is used throughout Warp and M. When weighting tilt movie frames to produce the movie average during e.g. fs_motion_and_ctf, dose_frame(n) - dose_frame(0) (where dose_frame(0) is the accumulated dose from the beginning of the tilt series by the time the first frame of that movie is acquired) is applied since B factors are additive and the tilt series processing will apply dose_frame(0) to the pre-weighted tilt image later.

[Maurice Frijns]

Hi Dimitri and Alister,

Thanks for the responses, very insightful!

Cheers, 

Maurice 

Op ma 13 okt 2025 om 03:56 schreef teg...@gmail.com <teg...@gmail.com>:

To view this discussion visit https://groups.google.com/d/msgid/warp-em/a18b8fcc-63df-4f33-bb0c-3ece84b7a274n%40googlegroups.com.