[R] solicit help to read in 384 plate color image

Mon Apr 7 10:00:00 CEST 2014

Hi

Yes I know about EBImage. It was rather too complicated for some simple tasks reading image, performing rowwise/colwise computations and summing or averaging of rows or columns which was my task (and I had some code from ancient times which used rimage :). However when I read introduction to EBImage it seems that it can do the same job (after some learning from my side :).

Thanks
Petr

> -----Original Message-----
> From: Spencer Graves [mailto:spencer.graves at structuremonitoring.com]
> Sent: Monday, April 07, 2014 9:12 AM
> To: PIKAL Petr; Waverley @ Palo Alto; r-help
> Subject: Re: [R] solicit help to read in 384 plate color image
>
>        Have you considered the Bioconductor package "EBImage"?  See
> "www.bioconductor.org/packages/release/bioc/html/EBImage.html".
>
>
>        I found it using findFn{sos}.  It seems well developed, well
> maintained AND includes a vignette that simplifies the job of learning
> how to use it.
>
>
>        Hope this helps.
>        Spencer
>
>
> On 4/6/2014 11:56 PM, PIKAL Petr wrote:
> > Hi
> >
> > There was package rimage which could read jpeg file in colours and
> manipulate with it. However it is not actively maintained and therefore
> it does not work in recent versions of R. I believe that R 2.14.0 is
> the last version able to use rimage. It was quite simple and I was
> tempted to start its maintenance but I do not use it often and so my
> interest ceased. If you wanted to try it you need to install this old
> version, install rimage. After that you can read your images in this
> old version, preprocess it with rimage and save result for use in new R
> version.
> >
> > Regards
> > Petr
> >
> > PS. If you do not find rimage in CRAN I can send you a zip file.
> >
> >
> >
> >> -----Original Message-----
> >> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> >> project.org] On Behalf Of Waverley @ Palo Alto
> >> Sent: Friday, April 04, 2014 10:28 PM
> >> To: r-help
> >> Subject: [R] solicit help to read in 384 plate color image
> >>
> >> Hi,
> >>
> >> I am doing an experiment which results different colors of different
> >> intensities in the 384 micro titer plate.
> >>
> >> I took a picture of the plate by scanning in the image as a jpeg
> file
> >> and now I want to
> >>
> >> 1. read in the image file
> >> 2. grid the content
> >> 3. need to extract the intensity and color of each well.
> >>
> >> Is there a R package I can use for that? there is a package called
> >> "gitter"
> >> which is almost satisfying my needs. However, it can only read in
> grey
> >> values and no colors.
> >>
> >> If someone has the code, please share.
> >>
> >> --
> >>
> >> Thanks.
> >>
> >> waverley
> >>
> >>        [[alternative HTML version deleted]]
> >>
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- a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany příjemce s dodatkem či odchylkou.
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- odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu případně osobě, kterou adresát zastupuje, předloženy nebo jejich existence je adresátovi či osobě jím zastoupené známá.

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