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Hi David,<br>
<br>
Were the images recorded with different image shifts? If that was
the case, the stage coordinates alone would not be sufficient to
predict the pixel positions of the data acquisition images on the
grid square image. It could also be a combination of inaccurate
pixel size and defocusing, image rotation, ... .<br>
<br>
We earlier reported two methods to establish a correlation between
low-mag and high-mag images (these roughly correspond to your grid
square and data acquisition images, respectively), see Coordinate
transformation based cryo-correlative methods for electron
tomography and focused ion beam milling, Fukuda et al 2014. Feel
free to contact me if you need more info.<br>
<br>
Best,<br>
Vladan <br>
<br>
<div class="moz-cite-prefix">On 06/09/2023 18:29, Morgan, David Gene
wrote:<br>
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Hi,</div>
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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.<br>
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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.<br>
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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).</div>
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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).</div>
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Has anyone attempted anything like this, or does anyone have a
clue about why the results seem so "off"?</div>
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Thanks in advance for any insights.<br>
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David Gene Morgan<br>
Electron Microscopy Center<br>
047E Simon Hall<br>
IU Bloomington<br>
812 856 1457 (office)<br>
812 856 3221 (3200)<br>
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