analyze different marked cells

[Jörg Walter]

Hello everyone,

I try to discriminate between different marked cells (see attached). so i first substracted the background and then did a color threshold. but now i have the problem that there are not only the marked cells i want to count but also some edges of the other cells (2nd attachement). is there any way to get rid of them?

best,
jörg

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[Ignacio Arganda-Carreras]

Hello Jorg,

I'm not sure which cells you want to keep, but you might want to give a try
to the SIOX segmentation plugin:

http://fiji.sc/SIOX

Or the Trainable Weka Segmentation:

http://fiji.sc/Trainable_Weka_Segmentation

Cheers!

ignacio


On Thu, Dec 11, 2014 at 10:48 AM, Jörg <[hidden email]>
wrote:

>
> Hello everyone,
>
> I try to discriminate between different marked cells (see attached). so i
> first substracted the background and then did a color threshold. but now i
> have the problem that there are not only the marked cells i want to count
> but also some edges of the other cells (2nd attachement). is there any way
> to get rid of them?
>
> best,
> jörg
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA

Phone: [phone]
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

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[Guilherme Barbosa]

Hello Jorg

I am not a specialist in programing, but what i would try to do if I were you is:

Try to get a ROI for each cell, using threshold -> analyst particle -> add to ROI, then after that I would split color get the channel that better represents purple and the measure the “amount” of purple in each cell… after it you would have a table on excel with you could determinate the threshold of stain that better represents your cell…. You can double check if the threshold is good, and after it you just ask the excel to count how many cells are under that score.

It looks like a lot of work but you can make it more automatic once you the everything right.

I don’t know if my low experience will help you. But good luck.

Guilherme O. Barbosa.
State University of Campinas
Sao Paulo Brazil

> On Dec 11, 2014, at 1:48 AM, Jörg <[hidden email]> wrote:
>
> Hello everyone,
>
> I try to discriminate between different marked cells (see attached). so i first substracted the background and then did a color threshold. but now i have the problem that there are not only the marked cells i want to count but also some edges of the other cells (2nd attachement). is there any way to get rid of them?
>
> best,
> jörg
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> <Testmaus1.png><Testmaus2.png>

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[Joel Sheffield]

Hi Jorg,

I am as puzzled as the others about which criteria you are using to
discriminate between the two kinds of labeling.  As I see it, it appears
that the cells that you do not want to count have a large amount of
staining, that fills the nucleus, and the ones that you want to count have
much smaller regions of stain.  Those regions, however, appear to be
contiguous --that is they are not composed of small spots.  So, I carried
out a color threshold on the original image, selecting only on hue, and was
able to see the populations of cells with large nuclei, and those with
small regions of stain. Note that I kept the brightness and saturation
settings wide open.  I assume that I could then isolate the ones that I
care about by selecting a size criterion in the Analyze Particles routine.
Or is this not what you had in mind?

Joel[image: Inline image 1]Note, I k



Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  *http://tinyurl.com/khbouft <http://tinyurl.com/khbouft>*

On Thu, Dec 11, 2014 at 4:48 AM, Jörg <[hidden email]>
wrote:

> Hello everyone,
>
> I try to discriminate between different marked cells (see attached). so i
> first substracted the background and then did a color threshold. but now i
> have the problem that there are not only the marked cells i want to count
> but also some edges of the other cells (2nd attachement). is there any way
> to get rid of them?
>
> best,
> jörg
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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