How do I know what `exposure` should be `create_settings`?

[Spencer Rothfuss]

Hello!

Simple question that I can't find an answer to. When running `WarpTools create_settings` an `--exposure` argument is required. The help says:

--exposure             Default: 1. Overall exposure per Angstrom^2...

I'm assuming this means "total dose per tilt" not just "total dose." If so, how do I know what to set for that value? Is it reported in the mdoc? Can it be calculated in some other way? In the quick start, `--exposure` is set to 2.64 but no params in those mdocs are equal 2.64. Thanks!

[Pranav Shah]

That value is the total dose per tilt eg 2.64,3.0 etc. typically this value is referred to as the ExposureDose in the mdoc file. Your facility manager should be able to provide you that number.

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

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[Spencer Rothfuss]

Thanks to Pranav Shah and Alice Eruera for helping out here. They have confirmed that WarpTools expects dose per tilt for the `--exposure` argument.

Regarding what ExposureDose means, after conferring with our facility and the ThermoFisher tomography team, I've confirmed that, in Tomo 5, ExposureDose records dose per tilt. However, a potentially helpful caveat is that ExposureDose typically records dose at camera (i.e. dose over sample). Dose at camera is noteworthy because that value is lower than the dose that actually hits the sample and because it is inconsistent across images in a tilt series (i.e. it decreases with increasing tilt angle). In the most recent versions of Tomo (5.23 and later), Falcon cameras can remember dose over vacuum from the Exposure preset and report that in the mdoc, but all other cameras and versions only report dose at camera over sample.

There's some potential issues with how our particular scopes are writing ExposureDose, if we get to the bottom of that and there's anything general to share I'll post a follow up.

Gratefully,
Spencer