[3dem] EPU and serialEM

[Sylvain Trepout]

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
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>
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