pattern evaluation in electron microscopy images

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pattern evaluation in electron microscopy images

PIKAL Petr
Dear all

I enclose 3 electron microscope images in which I would like to evaluate plane spacing.

Before I start to dig deeper and use trial and error in trying to find some packages/functions for such pattern evaluation in electron microscopy pictures I would like to ask if anybody could point me to suitable packages/functions.

I am aware of EBImage package for general purpose image manipulation, but it does not have such functionality.

Best regards
Petr

If images did not came through please use this link:
Stáhnout soubory<https://uschovna.agrofert.cz/dshosts/getfiles.aspx?fip=2475efa6-a77b-4ff6-8155-d9302e7b151b>.

Osobní údaje: Informace o zpracování a ochraně osobních údajů obchodních partnerů PRECHEZA a.s. jsou zveřejněny na: https://www.precheza.cz/zasady-ochrany-osobnich-udaju/ | Information about processing and protection of business partner's personal data are available on website: https://www.precheza.cz/en/personal-data-protection-principles/
Důvěrnost: Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a podléhají tomuto právně závaznému prohláąení o vyloučení odpovědnosti: https://www.precheza.cz/01-dovetek/ | This email and any documents attached to it may be confidential and are subject to the legally binding disclaimer: https://www.precheza.cz/en/01-disclaimer/

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Re: pattern evaluation in electron microscopy images

S Ellison-2
Not really my field, but would you not approach this using FFT on selected regions?

I think IMageJ has some capability in that area; see example at https://imagej.nih.gov/ij/docs/examples/tem/.

Steve Ellison



> -----Original Message-----
> From: R-help [mailto:[hidden email]] On Behalf Of PIKAL Petr
> Sent: 08 February 2019 09:54
> To: [hidden email]
> Subject: [R] pattern evaluation in electron microscopy images
>
> Dear all
>
> I enclose 3 electron microscope images in which I would like to evaluate
> plane spacing.
>
> Before I start to dig deeper and use trial and error in trying to find some
> packages/functions for such pattern evaluation in electron microscopy
> pictures I would like to ask if anybody could point me to suitable
> packages/functions.
>
> I am aware of EBImage package for general purpose image manipulation, but
> it does not have such functionality.
>
> Best regards
> Petr
>
> If images did not came through please use this link:
> Stáhnout
> soubory<https://uschovna.agrofert.cz/dshosts/getfiles.aspx?fip=2475efa6-
> a77b-4ff6-8155-d9302e7b151b>.
>
> Osobní údaje: Informace o zpracování a ochraně osobních údajů obchodních
> partnerů PRECHEZA a.s. jsou zveřejněny na:
> https://www.precheza.cz/zasady-ochrany-osobnich-udaju/ | Information
> about processing and protection of business partner's personal data are
> available on website: https://www.precheza.cz/en/personal-data-
> protection-principles/
> Důvěrnost: Tento e-mail a jakékoliv k němu připojené dokumenty jsou
> důvěrné a podléhají tomuto právně závaznému prohláąení o vyloučení
> odpovědnosti: https://www.precheza.cz/01-dovetek/ | This email and any
> documents attached to it may be confidential and are subject to the legally
> binding disclaimer: https://www.precheza.cz/en/01-disclaimer/
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> and provide commented, minimal, self-contained, reproducible code.


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Re: pattern evaluation in electron microscopy images

PIKAL Petr
Hallo Steve.

Thank you for pointing to ImageJ, I will try to inspect it. I expected that somebody in R comunity automated such procedure within some R package, but it is probably too specialised.

S pozdravem | Best Regards
RNDr. Petr PIKAL
Vedoucí Výzkumu a vývoje | Research Manager
PRECHEZA a.s.
nábř. Dr. Edvarda Beneše 1170/24 | 750 02 Přerov | Czech Republic
Tel: +420 581 252 256 | GSM: +420 724 008 364
[hidden email] | www.precheza.cz

Osobní údaje: Informace o zpracování a ochraně osobních údajů obchodních partnerů PRECHEZA a.s. jsou zveřejněny na: https://www.precheza.cz/zasady-ochrany-osobnich-udaju/ | Information about processing and protection of business partner's personal data are available on website: https://www.precheza.cz/en/personal-data-protection-principles/
Důvěrnost: Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a podléhají tomuto právně závaznému prohlášení o vyloučení odpovědnosti: https://www.precheza.cz/01-dovetek/ | This email and any documents attached to it may be confidential and are subject to the legally binding disclaimer: https://www.precheza.cz/en/01-disclaimer/

> -----Original Message-----
> From: S Ellison <[hidden email]>
> Sent: Monday, February 11, 2019 12:54 PM
> To: PIKAL Petr <[hidden email]>; [hidden email]
> Subject: RE: pattern evaluation in electron microscopy images
>
> Not really my field, but would you not approach this using FFT on selected
> regions?
>
> I think IMageJ has some capability in that area; see example at
> https://imagej.nih.gov/ij/docs/examples/tem/.
>
> Steve Ellison
>
>
>
> > -----Original Message-----
> > From: R-help [mailto:[hidden email]] On Behalf Of PIKAL
> > Petr
> > Sent: 08 February 2019 09:54
> > To: [hidden email]
> > Subject: [R] pattern evaluation in electron microscopy images
> >
> > Dear all
> >
> > I enclose 3 electron microscope images in which I would like to
> > evaluate plane spacing.
> >
> > Before I start to dig deeper and use trial and error in trying to find
> > some packages/functions for such pattern evaluation in electron
> > microscopy pictures I would like to ask if anybody could point me to
> > suitable packages/functions.
> >
> > I am aware of EBImage package for general purpose image manipulation,
> > but it does not have such functionality.
> >
> > Best regards
> > Petr
> >
> > If images did not came through please use this link:
> > Stáhnout
> > soubory<https://uschovna.agrofert.cz/dshosts/getfiles.aspx?fip=2475efa
> > 6-
> > a77b-4ff6-8155-d9302e7b151b>.
> >
> > Osobní údaje: Informace o zpracování a ochraně osobních údajů
> > obchodních partnerů PRECHEZA a.s. jsou zveřejněny na:
> > https://www.precheza.cz/zasady-ochrany-osobnich-udaju/ | Information
> > about processing and protection of business partner's personal data
> > are available on website: https://www.precheza.cz/en/personal-data-
> > protection-principles/
> > Důvěrnost: Tento e-mail a jakékoliv k němu připojené dokumenty jsou
> > důvěrné a podléhají tomuto právně závaznému prohláąení o vyloučení
> > odpovědnosti: https://www.precheza.cz/01-dovetek/ | This email and any
> > documents attached to it may be confidential and are subject to the
> > legally binding disclaimer: https://www.precheza.cz/en/01-disclaimer/
> >
> > ______________________________________________
> > [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-
> > guide.html and provide commented, minimal, self-contained,
> > reproducible code.
>
>
> *****************************************************************
> **
> This email and any attachments are confidential. Any u...{{dropped:10}}

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.