<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
</head>
<body>
<div style="font-family: inherit; font-size: inherit; color: inherit; background-color: transparent;">
</div>
<div style="font-family: inherit; font-size: inherit; color: inherit; background-color: transparent;">
Wim,</div>
<div style="font-family: inherit; font-size: inherit; color: inherit; background-color: transparent;">
<br>
</div>
<div style="font-family: inherit; font-size: inherit; color: inherit; background-color: transparent;">
Thanks so much. I'm out of the office for several days but will check this out when I return.<br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div name="divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0">
<div name="divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0">
-- </div>
<div name="divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0">
politics is more difficult than physics.</div>
<div name="divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0">
A. Einstein</div>
<div name="divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0">
<br>
<div name="divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0">
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>
<a href="https://urldefense.com/v3/__http://iubemcenter.indiana.edu__;!!Mih3wA!DgLIzWb6yrZycU9SOJme2vR5c8vGAtUL5RcAINm5UY0e2yc0S5Fautw-EFb9Ep8r7A7kGrNnfKOw6W2QMaEZsf8$">http://iubemcenter.indiana.edu</a></div>
</div>
</div>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> serialem@colorado.edu <serialem@colorado.edu> on behalf of Wim Hagen <wimhag@gmail.com><br>
<b>Sent:</b> Wednesday, September 6, 2023 4:28 PM<br>
<b>To:</b> SerialEM <serialem@colorado.edu>; 3dem@ncmir.ucsd.edu <3dem@ncmir.ucsd.edu><br>
<b>Subject:</b> [External] Re: EPU and serialEM</font>
<div> </div>
</div>
<div style="line-break:after-white-space">
<p></p>
<div style="background-color:#FFEB9C; width:100%; border-style:solid; border-color:#9C6500; border-width:1pt; padding:2pt; font-size:10pt; line-height:12pt; font-family:Calibri; color:Black; text-align:left">
This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources.</div>
<br>
<p></p>
<div>
<div>Hi,</div>
<div>\</div>
<div>Maybe check how others tackled similar things:</div>
<div><br>
</div>
<a href="https://urldefense.com/v3/__https://github.com/kylelmorris/epubrowser__;!!Mih3wA!DgLIzWb6yrZycU9SOJme2vR5c8vGAtUL5RcAINm5UY0e2yc0S5Fautw-EFb9Ep8r7A7kGrNnfKOw6W2Qsou4PP4$" originalsrc="https://github.com/kylelmorris/epubrowser" shash="zJcv0VZEap5RM5gKxBEX8cg6d135U6NW0edeuiwsB19OsV+tgf/9sAyYAhgjGJwN66Ti9GQiFrjj7ii6LSG0uGJ+9XfO1UYY+ALWAnZrSy8/AOLzhTG9WonUMzEzqkPjZ5/cDdpkEIFi0k+phQCX7jROc0OLqYNK3nWFdsGwThc=">https://github.com/kylelmorris/epubrowser</a>
<div><br>
</div>
<div><a href="https://urldefense.com/v3/__https://github.com/kylelmorris/epubrowser/blob/main/EPU_browser.mp4__;!!Mih3wA!DgLIzWb6yrZycU9SOJme2vR5c8vGAtUL5RcAINm5UY0e2yc0S5Fautw-EFb9Ep8r7A7kGrNnfKOw6W2Q_MYVXJQ$" originalsrc="https://github.com/kylelmorris/epubrowser/blob/main/EPU_browser.mp4" shash="H1qsgzxUYiSj8i6O3nRABm9uFhass25D5A8eiuUiefu/yaqnJr5+FTD+GOMaw69IFXEAYsjHsGeK8UZLrnWbaUV2nd13d0kO/KYnFcF7vTl06TGIRM9jqUwBAIPy5/xkNsbD1BxEmgOI99768vajasx8EODAhFglwZRz+sLDLJo=">https://github.com/kylelmorris/epubrowser/blob/main/EPU_browser.mp4</a></div>
<div><br>
</div>
<div>Best,</div>
<div><br>
</div>
<div>Wim</div>
<div><br>
<blockquote type="cite">
<div>On 6. Sep 2023, at 18:29, Morgan, David Gene <dagmorga@indiana.edu> wrote:</div>
<br class="x_Apple-interchange-newline">
<div>
<div class="x_elementToProof" style="font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; font-family:Calibri,Helvetica,sans-serif; font-size:12pt">
Hi,</div>
<div class="x_elementToProof" style="font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; font-family:Calibri,Helvetica,sans-serif; font-size:12pt">
<br>
</div>
<div class="x_elementToProof" style="font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; font-family:Calibri,Helvetica,sans-serif; font-size:12pt">
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>
</div>
<div class="x_elementToProof" style="font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; font-family:Calibri,Helvetica,sans-serif; font-size:12pt">
<br>
</div>
<div class="x_elementToProof" style="font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; font-family:Calibri,Helvetica,sans-serif; font-size:12pt">
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>
</div>
<div class="x_elementToProof" style="font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; font-family:Calibri,Helvetica,sans-serif; font-size:12pt">
<br>
</div>
<div class="x_elementToProof" style="font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; font-family:Calibri,Helvetica,sans-serif; font-size:12pt">
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>
<div class="x_elementToProof" style="font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; font-family:Calibri,Helvetica,sans-serif; font-size:12pt">
<br>
</div>
<div class="x_elementToProof" style="font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; font-family:Calibri,Helvetica,sans-serif; font-size:12pt">
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>
<div class="x_elementToProof" style="font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; font-family:Calibri,Helvetica,sans-serif; font-size:12pt">
<br>
</div>
<div class="x_elementToProof" style="font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; font-family:Calibri,Helvetica,sans-serif; font-size:12pt">
Has anyone attempted anything like this, or does anyone have a clue about why the results seem so "off"?</div>
<div class="x_elementToProof" style="font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; font-family:Calibri,Helvetica,sans-serif; font-size:12pt">
<br>
</div>
<div class="x_elementToProof" style="font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; font-family:Calibri,Helvetica,sans-serif; font-size:12pt">
Thanks in advance for any insights.<br>
</div>
<div class="x_elementToProof" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt"><br>
</div>
<div id="x_Signature">
<div>
<div name="x_divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; margin:0px">
<div name="x_divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; margin:0px">
-- </div>
<div name="x_divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; margin:0px">
politics is more difficult than physics.</div>
<div name="x_divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; margin:0px">
A. Einstein</div>
<div name="x_divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; margin:0px">
<br>
<div name="x_divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; margin:0px">
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 class="x_Apple-converted-space"> </span><a href="https://urldefense.com/v3/__http://iubemcenter.indiana.edu/__;!!Mih3wA!DgLIzWb6yrZycU9SOJme2vR5c8vGAtUL5RcAINm5UY0e2yc0S5Fautw-EFb9Ep8r7A7kGrNnfKOw6W2Q_G30Hl0$" originalsrc="http://iubemcenter.indiana.edu/" shash="PXo73A3tU8Tn/uN1GgUWv9+ANcvFKMCJ1Igx2vhh1Ued+4msyJn7XFuMRdbe0Zi0DPesD0wVaywGJGrsDhc0WolUt/3qiNW1F0MK6aKNjRmPXu8SCicid9EzKBEBjasyY6XnnRbikKZpoilrqKaQNtcVDJotdPNmLW3u7SxjPjk=">http://iubemcenter.indiana.edu</a></div>
</div>
</div>
</div>
</div>
</div>
<p style="margin-top:0px; margin-bottom:0px; font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
</p>
<span style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">--<span class="x_Apple-converted-space"> </span></span><br style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">To
post to this group, send email to<span class="x_Apple-converted-space"> </span></span><a href="mailto:serialem@colorado.edu" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">serialem@colorado.edu</a><br style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">To
unsubscribe from this group, send email to<span class="x_Apple-converted-space"> </span></span><a href="mailto:serialem+unsubscribe@colorado.edu" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">serialem+unsubscribe@colorado.edu</a><br style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">---<span class="x_Apple-converted-space"> </span></span><br style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">To
unsubscribe from this group and stop receiving emails from it, send an email to<span class="x_Apple-converted-space"> </span></span><a href="mailto:serialem+unsubscribe@colorado.edu" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">serialem+unsubscribe@colorado.edu</a><span style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">.</span></div>
</blockquote>
</div>
<br>
<p></p>
-- <br>
To post to this group, send email to serialem@colorado.edu<br>
To unsubscribe from this group, send email to serialem+unsubscribe@colorado.edu<br>
--- <br>
To unsubscribe from this group and stop receiving emails from it, send an email to
<a href="mailto:serialem+unsubscribe@colorado.edu">serialem+unsubscribe@colorado.edu</a>.<br>
</div>
</div>
</body>
</html>