[3dem] EPU and serialEM
Sylvain Trepout
sylvain.trepout at monash.edu
Wed Sep 6 13:13:41 PDT 2023
Hi David,
Did you try changing the origin of the image (pixel 1,1 or 0,0) from the
bottom left corner to the top left corner ? Or the other way around?
Cheers,
Sylvain
PhD
Research Fellow - Microscopy Australia
Monash University
Ramaciotti Centre for Cryo-EM
G92, 15 Innovation Walk, Clayton Campus
Victoria, 3800 Australia
On Thu, 7 Sept 2023, 2:29 am Morgan, David Gene, <dagmorga at indiana.edu>
wrote:
> Hi,
>
> I'm cross-posting this both to the 3dem and the serialEM lists in the hope
> that someone may be able to help me. It concerns data from our Talos
> Arctica acquired with EPU that I would like to be able to make serialEM
> aware of.
>
> For reasons I won't bore you with, I am trying to take the stage positions
> acquired during an EPU data acquisition run and map them onto the image of
> a grid square also acquired during that same run. In other words, from the
> XML files that EPU produces, I can extract the stage coordinates of both
> the data acquisitions and the grid square image, and I want to "unify" them
> at the level of the grid square image.
>
> With a bit of math, I can convert the stage coordinates of the
> acquisitions into pixel coordinates for the grid square image. I'm
> initially overlaying these coordinates onto the grid square image using
> IMOD, after which I will move to making serialEM aware of this information.
> When I map locations onto the grid square image, the resulting locations
> don't make much sense... For example, some of the acquisitions are deep
> into grid bars and none of them align with holes in the holey carbon film.
> Something is clearly very wrong (and I don't think it's the relatively
> simple math).
>
> It could be a simple as an incorrect pixel size for the grid square image
> (but it would require that the pixel size be incredibly wrong), or it may
> be something going on inside EPU that I don't understand (like the
> application of some sort of transformation between the EPU imaging states -
> I'm thinking of the steps to align the various images).
>
> Has anyone attempted anything like this, or does anyone have a clue about
> why the results seem so "off"?
>
> Thanks in advance for any insights.
>
> --
> politics is more difficult than physics.
> A. Einstein
>
> David Gene Morgan
> Electron Microscopy Center
> 047E Simon Hall
> IU Bloomington
> 812 856 1457 (office)
> 812 856 3221 (3200)
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>
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