[3dem] 3dem Digest, Vol 193, Issue 10

Mon Sep 11 03:49:28 PDT 2023

Hi David, Wim,

Thanks for the link @wim!

@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.

Best wishes,
Kyle

From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of 3dem-request at ncmir.ucsd.edu <3dem-request at ncmir.ucsd.edu>
Date: Saturday, 9 September 2023 at 19:05
To: 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>
Subject: 3dem Digest, Vol 193, Issue 10
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Today's Topics:

   1. Re: [External] Re: EPU and serialEM (Morgan, David Gene)
   2. Re: glow discharge carbon coated grids several times?
      (Daniel Asarnow)
   3. Re: glow discharge carbon coated grids several times?
      (Haaris Ahsan Safdari)

----------------------------------------------------------------------

Message: 1
Date: Sat, 9 Sep 2023 01:50:41 +0000
From: "Morgan, David Gene" <dagmorga at indiana.edu>
To: Wim Hagen <wimhag at gmail.com>, SerialEM <serialem at colorado.edu>,
        "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] [External] Re: EPU and serialEM
Message-ID:
        <BY5PR08MB64072EC1652489E3B2D608C5D0ECA at BY5PR08MB6407.namprd08.prod.outlook.com>

Content-Type: text/plain; charset="us-ascii"

Wim,

Thanks so much. I'm out of the office for several days but will check this out when I return.

--
    politics is more difficult than physics.
                                             A. Einstein

            David Gene Morgan
        Electron Microscopy Center
             047E Simon Hall
             IU Bloomington
          812 856 1457 (office)
          812 856 3221 (3200)
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________________________________
From: serialem at colorado.edu <serialem at colorado.edu> on behalf of Wim Hagen <wimhag at gmail.com>
Sent: Wednesday, September 6, 2023 4:28 PM
To: SerialEM <serialem at colorado.edu>; 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>
Subject: [External] Re: EPU and serialEM

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Hi,
\
Maybe check how others tackled similar things:

https://urldefense.com/v3/__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__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU!!Mih3wA!DSDlc5wAJp-oGh_yCtpW7SYrQo4WA5B-FE3cWpmGbvf9B7FhJSM7WYdUbG8NWHjXP7LJ0v5qDK-UCFpoI8PXgfMy1A41Xg$ <https://urldefense.com/v3/__https://github.com/kylelmorris/epubrowser__;!!Mih3wA!DgLIzWb6yrZycU9SOJme2vR5c8vGAtUL5RcAINm5UY0e2yc0S5Fautw-EFb9Ep8r7A7kGrNnfKOw6W2Qsou4PP4$>

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Best,

Wim

On 6. Sep 2023, at 18:29, 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
          812 856 1457 (office)
          812 856 3221 (3200)
      https://urldefense.com/v3/__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__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!DSDlc5wAJp-oGh_yCtpW7SYrQo4WA5B-FE3cWpmGbvf9B7FhJSM7WYdUbG8NWHjXP7LJ0v5qDK-UCFpoI8PXgfO7eFvooQ$ <https://urldefense.com/v3/__http://iubemcenter.indiana.edu__;!!Mih3wA!DgLIzWb6yrZycU9SOJme2vR5c8vGAtUL5RcAINm5UY0e2yc0S5Fautw-EFb9Ep8r7A7kGrNnfKOw6W2QMaEZsf8$> <https://urldefense.com/v3/__https://eur03.safelinks.protection.outlook.com/?url=https*3A*2F*2Furldefense.com*2Fv3*2F__http*3A*2F*2Fiubemcenter.indiana.edu*2F__*3B!!Mih3wA!DgLIzWb6yrZycU9SOJme2vR5c8vGAtUL5RcAINm5UY0e2yc0S5Fautw-EFb9Ep8r7A7kGrNnfKOw6W2Q_G30Hl0*24&data=05*7C01*7Ckyle.morris*40diamond.ac.uk*7C363afa7237b54821973008dbb15f5401*7C9d27ba7401004d0d81ff1d728dae8df6*7C0*7C0*7C638298795227889954*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=KMnhHS2nlsamy*2B4YYozi*2BagBXy8vMJr6*2BYE*2BWHCUfLU*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!DSDlc5wAJp-oGh_yCtpW7SYrQo4WA5B-FE3cWpmGbvf9B7FhJSM7WYdUbG8NWHjXP7LJ0v5qDK-UCFpoI8PXgfPODPTLAQ$  >

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