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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;mso-fareast-language:EN-US">Hi David, Wim,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;mso-fareast-language:EN-US">Thanks for the link @wim!
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;mso-fareast-language:EN-US">@David - Gosh, that repo is from a while ago now.. it served the purpose of visually contextualising a data acquisition with respect to the square it came from but
I don’t think I went as far as ‘plotting’ the data acquisition coordinate on the square image as you are trying. Others have taken this further though in projects that are soon to be but not yet published, happy to discuss offline if it helps.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;mso-fareast-language:EN-US">Best wishes,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;mso-fareast-language:EN-US">Kyle<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">3dem <3dem-bounces@ncmir.ucsd.edu> on behalf of 3dem-request@ncmir.ucsd.edu <3dem-request@ncmir.ucsd.edu><br>
<b>Date: </b>Saturday, 9 September 2023 at 19:05<br>
<b>To: </b>3dem@ncmir.ucsd.edu <3dem@ncmir.ucsd.edu><br>
<b>Subject: </b>3dem Digest, Vol 193, Issue 10<o:p></o:p></span></p>
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Today's Topics:<br>
<br>
1. Re: [External] Re: EPU and serialEM (Morgan, David Gene)<br>
2. Re: glow discharge carbon coated grids several times?<br>
(Daniel Asarnow)<br>
3. Re: glow discharge carbon coated grids several times?<br>
(Haaris Ahsan Safdari)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Sat, 9 Sep 2023 01:50:41 +0000<br>
From: "Morgan, David Gene" <dagmorga@indiana.edu><br>
To: Wim Hagen <wimhag@gmail.com>, SerialEM <serialem@colorado.edu>,<br>
"3dem@ncmir.ucsd.edu" <3dem@ncmir.ucsd.edu><br>
Subject: Re: [3dem] [External] Re: EPU and serialEM<br>
Message-ID:<br>
<BY5PR08MB64072EC1652489E3B2D608C5D0ECA@BY5PR08MB6407.namprd08.prod.outlook.com><br>
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Content-Type: text/plain; charset="us-ascii"<br>
<br>
Wim,<br>
<br>
Thanks so much. I'm out of the office for several days but will check this out when I return.<br>
<br>
<br>
--<br>
politics is more difficult than physics.<br>
A. Einstein<br>
<br>
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>
</span><a href="https://urldefense.com/v3/__http://iubemcenter.indiana.edu__;!!Mih3wA!DgLIzWb6yrZycU9SOJme2vR5c8vGAtUL5RcAINm5UY0e2yc0S5Fautw-EFb9Ep8r7A7kGrNnfKOw6W2QMaEZsf8$"><span style="font-size:11.0pt">https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Fiubemcenter.indiana.edu__%3B!!Mih3wA!DgLIzWb6yrZycU9SOJme2vR5c8vGAtUL5RcAINm5UY0e2yc0S5Fautw-EFb9Ep8r7A7kGrNnfKOw6W2QMaEZsf8%24&data=05%7C01%7Ckyle.morris%40diamond.ac.uk%7C363afa7237b54821973008dbb15f5401%7C9d27ba7401004d0d81ff1d728dae8df6%7C0%7C0%7C638298795227889954%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=oC7b79iRkzQbGL1zvgAbOK%2Fy8f6Oj1mxG1D9W7Fxb%2Fw%3D&reserved=0</span></a><span style="font-size:11.0pt">
<br>
________________________________<br>
From: serialem@colorado.edu <serialem@colorado.edu> on behalf of Wim Hagen <wimhag@gmail.com><br>
Sent: Wednesday, September 6, 2023 4:28 PM<br>
To: SerialEM <serialem@colorado.edu>; 3dem@ncmir.ucsd.edu <3dem@ncmir.ucsd.edu><br>
Subject: [External] Re: EPU and serialEM<br>
<br>
<br>
This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources.<br>
<br>
<br>
Hi,<br>
\<br>
Maybe check how others tackled similar things:<br>
<br>
</span><a href="https://urldefense.com/v3/__https://github.com/kylelmorris/epubrowser__;!!Mih3wA!DgLIzWb6yrZycU9SOJme2vR5c8vGAtUL5RcAINm5UY0e2yc0S5Fautw-EFb9Ep8r7A7kGrNnfKOw6W2Qsou4PP4$"><span style="font-size:11.0pt">https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fgithub.com%2Fkylelmorris%2Fepubrowser__%3B!!Mih3wA!DgLIzWb6yrZycU9SOJme2vR5c8vGAtUL5RcAINm5UY0e2yc0S5Fautw-EFb9Ep8r7A7kGrNnfKOw6W2Qsou4PP4%24&data=05%7C01%7Ckyle.morris%40diamond.ac.uk%7C363afa7237b54821973008dbb15f5401%7C9d27ba7401004d0d81ff1d728dae8df6%7C0%7C0%7C638298795227889954%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=6oRaT1S8E5Xmn78d%2FJIjTfgmYwgxCqb1O6KstV6gEjY%3D&reserved=0</span></a><span style="font-size:11.0pt">
<br>
<br>
</span><a href="https://urldefense.com/v3/__https://github.com/kylelmorris/epubrowser/blob/main/EPU_browser.mp4__;!!Mih3wA!DgLIzWb6yrZycU9SOJme2vR5c8vGAtUL5RcAINm5UY0e2yc0S5Fautw-EFb9Ep8r7A7kGrNnfKOw6W2Q_MYVXJQ$"><span style="font-size:11.0pt">https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fgithub.com%2Fkylelmorris%2Fepubrowser%2Fblob%2Fmain%2FEPU_browser.mp4__%3B!!Mih3wA!DgLIzWb6yrZycU9SOJme2vR5c8vGAtUL5RcAINm5UY0e2yc0S5Fautw-EFb9Ep8r7A7kGrNnfKOw6W2Q_MYVXJQ%24&data=05%7C01%7Ckyle.morris%40diamond.ac.uk%7C363afa7237b54821973008dbb15f5401%7C9d27ba7401004d0d81ff1d728dae8df6%7C0%7C0%7C638298795227889954%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=LqzMAAQGp6MhJdno3PNHFmLGrSHf%2FAO9YVw3bL%2FPfPA%3D&reserved=0</span></a><span style="font-size:11.0pt">
<br>
<br>
Best,<br>
<br>
Wim<br>
<br>
On 6. Sep 2023, at 18:29, Morgan, David Gene <dagmorga@indiana.edu> wrote:<br>
<br>
Hi,<br>
<br>
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>
<br>
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>
<br>
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).<br>
<br>
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).<br>
<br>
Has anyone attempted anything like this, or does anyone have a clue about why the results seem so "off"?<br>
<br>
Thanks in advance for any insights.<br>
<br>
--<br>
politics is more difficult than physics.<br>
A. Einstein<br>
<br>
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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