Should we remove the dose when dose has been applied...

[pconesa]

If we do dose weighted motion correction or if we do an imod dose filtering.....does is make sense to clear the dose information?

[azazellochg]

Not sure why would you do this? It's acquisition information. E.g. we dont remove tilt axis angle for aligned ts.

[pconesa]

If metadata describes the data, to me it make sense El sáb., 17 dic. 2022 18:42, Grigory Sharov ***@***.***> escribió:

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Not sure why would you do this? It's acquisition information. E.g. we dont remove tilt axis angle for aligned ts. — Reply to this email directly, view it on GitHub <#297 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAF7ZYNRYVTXFZZBUUE73R3WNX3SDANCNFSM6AAAAAAS5NIPVU> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[azazellochg]

True, then can we remove the tilt axis angle from an aligned ts? Should we remove ctf from ctf-corrected ts? For me, acquisition metadata should never be changed because it is related more to the experiment rather than the data itself. I don't see any problem of keeping the dose, ctf etc. Now we have flags for ctf corrected/aligned data. You can add one more if you like, though I think it's not necessary (e.g. in SPA there's no such problem of keeping the track what was dose weighted or not) Best regards, Grigory

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-------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: ***@***.***

On Sun, Dec 18, 2022 at 8:17 AM Pablo Conesa ***@***.***> wrote: If metadata describes the data, to me it make sense El sáb., 17 dic. 2022 18:42, Grigory Sharov ***@***.***> escribió: > Not sure why would you do this? It's acquisition information. E.g. we dont > remove tilt axis angle for aligned ts. > > — > Reply to this email directly, view it on GitHub > < #297 (comment) >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AAF7ZYNRYVTXFZZBUUE73R3WNX3SDANCNFSM6AAAAAAS5NIPVU > > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> > — Reply to this email directly, view it on GitHub <#297 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABVBPJVHYRU2HXOZXHCKFYLWN3CB7ANCNFSM6AAAAAAS5NIPVU> . You are receiving this because you commented.Message ID: ***@***.***>

[pconesa]

Thanks Grigory, this is why I was asking... We can use flags to assist the user.

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On 19/12/22 11:29, Grigory Sharov wrote: True, then can we remove the tilt axis angle from an aligned ts? Should we remove ctf from ctf-corrected ts? For me, acquisition metadata should never be changed because it is related more to the experiment rather than the data itself. I don't see any problem of keeping the dose, ctf etc. Now we have flags for ctf corrected/aligned data. You can add one more if you like, though I think it's not necessary (e.g. in SPA there's no such problem of keeping the track what was dose weighted or not) Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: ***@***.*** On Sun, Dec 18, 2022 at 8:17 AM Pablo Conesa ***@***.***> wrote: > If metadata describes the data, to me it make sense > > El sáb., 17 dic. 2022 18:42, Grigory Sharov ***@***.***> > escribió: > > > Not sure why would you do this? It's acquisition information. E.g. we > dont > > remove tilt axis angle for aligned ts. > > > > — > > Reply to this email directly, view it on GitHub > > < > #297 (comment) > >, > > or unsubscribe > > < > https://github.com/notifications/unsubscribe-auth/AAF7ZYNRYVTXFZZBUUE73R3WNX3SDANCNFSM6AAAAAAS5NIPVU > > > > . > > You are receiving this because you authored the thread.Message ID: > > ***@***.***> > > > > — > Reply to this email directly, view it on GitHub > <#297 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ABVBPJVHYRU2HXOZXHCKFYLWN3CB7ANCNFSM6AAAAAAS5NIPVU> > . > You are receiving this because you commented.Message ID: > ***@***.***> > — Reply to this email directly, view it on GitHub <#297 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAF7ZYKMIXQCVWFNTBXUXDLWOA2INANCNFSM6AAAAAAS5NIPVU>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[azazellochg]

I have to correct myself, removing (setting to 0) tilt axis for aligned TS is very important. Most imod-inspired software expects the tilt axis to be vertical (=0 in imod) before reconstruction. But this is not relevant for the issue here.

[pconesa]

Well, I think metadata should describe the data is associated with. A different question is if Acquisition is important to remain during the whole process. For example, once a tilt series is interpolated the transformation matrix is removed, same with the tilt axis you mentioned.
If dose has been "applied" ( in the same way the transformation or the tilt axis has been applied) then I think it should go away so latter protocols do not apply the dose again. Now, if the does has to remain anyway, we can use a flag (doseApplied?)

[azazellochg]

dose is used in polishing again

[pconesa]

yes, but for polishing you go back to the movies, right?

[azazellochg]

True. I've never used relion for tomo, so I dont know how it works. @JorMaister ?