[3dem] EPU and serialEM

[Schenk, Andreas]

Hi David,

I did something similar for visualization purposes. If you are only interested in the pixel coordinates for the acquisitions, you can read these out directly from the GridSquare dm file (in EPU 2.7 and newer). In there you can find a list of TargetLocations. Each target location has a set of x,y PixelLocations, which are relative to the grid square image. The PixelLocations should give you the center of the foil hole that was recorded. 

Best wishes,
Andreas



> 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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