Re: Cell counting

Posted by Jenny Mayböck on Apr 01, 2015; 8:24am
URL: http://imagej.273.s1.nabble.com/Cell-counting-tp5012266p5012286.html

Thank you so much! I will try your suggestions and I hope we can manage
somehow. If there are some further questions from my side I will contact
you again.

Thanks for once.

Good day to you all
Jenny

2015-04-01 1:14 GMT+02:00 Jacqui Ross <[hidden email]>:

> Hi Jenny,
>
> Just like to add my support to Andrei's recommendation that you use the
> Colour Deconvolution plugin for your initial segmentation. I couldn't tell
> from your images what resolution they are but hopefully you have the
> originals that you can use for the analysis.
>
> There are some instructions on our website that you can refer to if you
> need further assistance in using the plugin.
>
> Take a look here:
> https://www.fmhs.auckland.ac.nz/en/sms/about/our-departments/biomedical-imaging-research-unit/image-processing-and-analysis/analysis-resources.html
>
> Cheers,
>
> Jacqui
>
> Jacqueline Ross
> Biomedical Imaging Microscopist
> Biomedical Imaging Research Unit
> School of Medical Sciences
> Faculty of Medical & Health Sciences
> The University of Auckland
> Private Bag 92019
> Auckland 1142, NEW ZEALAND
>
> Tel: [phone]
> Fax: [phone]
>
> http://www.fmhs.auckland.ac.nz/sms/biru/
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Andrei Catalin Stefan
> Sent: Wednesday, 1 April 2015 8:58 a.m.
> To: [hidden email]
> Subject: Re: Cell counting
>
> Somehow I didn't added the link... But here it is:
>
> 1. *Correct the background illumination* (*see this LINK
> <
> http://imagejdocu.tudor.lu/doku.php?id=howto:working:how_to_correct_background_illumination_in_brightfield_microscopy
> >*
> ).
>
> 2015-03-31 19:29 GMT+01:00 Andrei Catalin Stefan <
> [hidden email]>:
>
> > Dear all,
> >
> > I am not an expert with ImageJ, but I would like to contribute to the
> > topic.
> > Before counting the cells, what I would do is:
> >
> > 1. *Correct the background illumination* (see this LINK, there are
> > ways so you need to see what is available and suits you).
> > 2. Use *Colour Deconvolution* (*see this LINK
> > <http://www.mecourse.com/landinig/software/cdeconv/cdeconv.html>*) or
> > *Trainable Weka Segmentation* (*see this LINK
> > <https://www.youtube.com/watch?v=8yfBHiGufFE>*) to isolate the cells
> > that interest you. There are also other means, but see what it works for
> you.
> > 3. Use ImageJ's built-in tool to count/analyse the cells.
> >
> > An other advice is to make sure the staining protocols, image
> > acquisition and image analysis is consistent so there is no room for
> major errors.
> >
> > Hope it helps,
> >
> >
> >
> > Best regards,
> > Andrei Stefan
> >
> > 2015-03-31 18:48 GMT+01:00 veraelisabeth <[hidden email]>:
> >
> >> Hi Jenny,
> >>
> >> I'm relatively new to imagej and I see some problems with it,
> >> regarding the subjectivity of it. But I'd try to separate the color
> >> channels (although I don't know if thats possible with your sort of
> >> image (I use immunofluorescence of cell cultures and it's possible)
> >>
> >> Then I would download the color pixel counter. Afterwards you could
> >> calculate all coloured pixels / mean pixels of one cell to get the
> >> number of cells
> >>
> >> But as I said. I'm quite new to imagej
> >>
> >>
> >>
> >> --
> >> View this message in context:
> >> http://imagej.1557.x6.nabble.com/Cell-counting-tp5012266p5012273.html
> >> Sent from the ImageJ mailing list archive at Nabble.com.
> >>
> >> --
> >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>
> >
> >
> >
> > --
> >
> > Andrei Cătălin ȘTEFAN, MRCVS, DVM, MVSc
> >
> > E-mail: [hidden email]
> >
> >
>
>
> --
>
> Andrei Cătălin ȘTEFAN, MRCVS, DVM, MVSc
>
> E-mail: [hidden email]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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