Help begineer to detect cells in petri dish

[MariaS]

Hello everybody!
I just started using ImageJ but I find it pretty hard to get the results I want.
I have for example this image from a petri dish with a filter with bacteria and I want to count the number of the cells. First I draw a circle to choose my area of interest, then i select Clear Outside and then I try with some filters and by adjusting the threshold to detect my cells. But the stripes of the filter on the petri dish create problems and I cannot find a way to remove them. Does anyone have some ideas that might help?

Thank you.
Maria

[Rasband, Wayne (NIH/NIMH) [E]]

> On Nov 10, 2015, at 9:59 AM, MariaS <[hidden email]> wrote:
>
> <http://imagej.1557.x6.nabble.com/file/n5014903/petri_dish.jpg>
>
> Hello everybody!
> I just started using ImageJ but I find it pretty hard to get the results I
> want.
> I have for example this image from a petri dish with a filter with bacteria
> and I want to count the number of the cells. First I draw a circle to choose
> my area of interest, then i select Clear Outside and then I try with some
> filters and by adjusting the threshold to detect my cells. But the stripes
> of the filter on the petri dish create problems and I cannot find a way to
> remove them. Does anyone have some ideas that might help?

Why not count manually? It only took me a couple of minutes to count the cells (86) using ImageJ's multi-point tool.

    http://wsr.imagej.net/images/petri_dish2.jpg

-wayne

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[MariaS]

Thanks for your answer!

The thing is that I have many images of this kind and in the end we want to create a Macro that can automatically count the cells. So the first step is at least to understand how to set the settings right manually. I did not think that it would be so hard to count the cells with ImageJ. And I started reading the guide of ImageJ but it is not really helpful in this case..

[Joel Sheffield]

Hi Maria,

It may be possible, with your image, to threshold the particles, and use
the discrimination functions of "Analyze Particles" to count only objects
of a given size range and/or circularity.  Part of the problem in that case
is that you have several examples of overlapping colonies.  In that case,
you could see if the watershed procedure would work around the grid lines.
Another issue is that your image is taken at quite low pixel density so
that discrimination is even more difficult.

That said, you might want to calculate the time that it would take to set
up an automatic system and set it against Wayne's suggestion. I suppose it
depends on what you mean by "many".


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 Tue, Nov 10, 2015 at 1:00 PM, MariaS <[hidden email]> wrote:

> Thanks for your answer!
>
> The thing is that I have many images of this kind and in the end we want to
> create a Macro that could automatically count the cells. So the first step
> is at least to understand how to set the settings right manually. I did not
> think that it would be so hard to count the cells with ImageJ. And I
> started
> reading the guide of ImageJ but it is not really helpful in this case..
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Help-begineer-to-detect-cells-in-petri-dish-tp5014903p5014906.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Herbie]

Dear Maria,

you wrote:
"I did not think that it would be so hard to count the cells with ImageJ."

Did you ever consider that the problem is with your image(s) and not
with ImageJ?

The image you've provided shows rather low spatial resolution, lots of
JEPG-artifacts, circular reflections, a high contrast grid, and
partially overlapping cells.

There is little chance to count the cells automatically and reliably, no
matter what software you use.

Best

Herbie

::::::::::::::::::::::::::::::::::::
Am 10.11.15 um 19:00 schrieb MariaS:
> Thanks for your answer!
>
> The thing is that I have many images of this kind and in the end we
> want to create a Macro that could automatically count the cells. So
> the first step is at least to understand how to set the settings
> right manually. I did not think that it would be so hard to count the
> cells with ImageJ. And I started reading the guide of ImageJ but it
> is not really helpful in this case.

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