Re: Cell counting

Posted by Jacqueline Ross on Mar 31, 2015; 11:14pm
URL: http://imagej.273.s1.nabble.com/Cell-counting-tp5012266p5012278.html

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]

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