Counting eggs

[oselm]

Hey,

I'm new and I'd like some suggestions about how to count eggs in this image.



My idea was to thershold the image and convert it to binary in order to count objects using the "analyze particle" command.

Any suggestion about how to process the image?

Many thanks

Oselm

[Cammer, Michael]

I would try to reshoot the picture with the light raking across from the side so each egg would have a bright spot at the center.  Then it's trivial to use Find Maxima to count the glaring spots which would be completely separate from each other.


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 Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone Medical Center
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          http://ocs.med.nyu.edu/microscopy & http://microscopynotes.com/

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of oselm
Sent: Thursday, July 09, 2015 10:06 AM
To: [hidden email]
Subject: Counting eggs

Hey,

I'm new and I'd like some suggestions about how to count eggs in this image.

<http://imagej.1557.x6.nabble.com/file/n5013485/eggs.jpg>

My idea was to thershold the image and convert it to binary in order to count objects using the "analyze particle" command.

Any suggestion about how to process the image?

Many thanks

Oselm



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[Kenneth Sloan-2]

I would cheat.  The eggs appear to be identical in size.

a) measure one egg in isolation and express it’s area in pixels
b) color threshold the image to get an Egg/non-Egg binary image
c) compute the area covered by eggs
d) report c/a

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Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.

> On Jul 9, 2015, at 09:06 , oselm <[hidden email]> wrote:
>
> Hey,
>
> I'm new and I'd like some suggestions about how to count eggs in this image.
>
> <http://imagej.1557.x6.nabble.com/file/n5013485/eggs.jpg>
>
> My idea was to thershold the image and convert it to binary in order to
> count objects using the "analyze particle" command.
>
> Any suggestion about how to process the image?
>
> Many thanks
>
> Oselm
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Counting-eggs-tp5013485.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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[Christopher Coulon-2]

If you can threshold the yellow area and that represents all your cells, then you can do an AnalyzeParticles and evaluate individual particles to determine the variation in size of the individual cells (those that happen to be separate from clumps of cells). You can write a method to find the most common size bin for your particles, and that will be your individual cell area range.  Divide the total yellow area, i.e., all cells, individual and clumped, by the mean of the individual cells and you get the estimated number of cells and error bars of the individual cell size variation.  This form of cheating is called “statistics” ;-)

> On Jul 9, 2015, at 1:24 PM, Kenneth Sloan <[hidden email]> wrote:
>
> I would cheat.  The eggs appear to be identical in size.
>
> a) measure one egg in isolation and express it’s area in pixels
> b) color threshold the image to get an Egg/non-Egg binary image
> c) compute the area covered by eggs
> d) report c/a
>
> --
> Kenneth Sloan
> [hidden email]
> Vision is the art of seeing what is invisible to others.
>
>
>
>
>> On Jul 9, 2015, at 09:06 , oselm <[hidden email]> wrote:
>>
>> Hey,
>>
>> I'm new and I'd like some suggestions about how to count eggs in this image.
>>
>> <http://imagej.1557.x6.nabble.com/file/n5013485/eggs.jpg>
>>
>> My idea was to thershold the image and convert it to binary in order to
>> count objects using the "analyze particle" command.
>>
>> Any suggestion about how to process the image?
>>
>> Many thanks
>>
>> Oselm
>>
>>
>>
>> --
>> View this message in context: http://imagej.1557.x6.nabble.com/Counting-eggs-tp5013485.html
>> Sent from the ImageJ mailing list archive at Nabble.com.
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[oselm]

Thank you for your answers! It was really helpful.

The main problem now is to find a way to threshold the picture. In particular, the yellow of the eggs is not homogenous across the picture and therefore it is not possible to distinguish between eggs in pale yellow and the spots between eggs in the agglomerate (also colored in pale yellow). Is there a way to threshold different zone of the picture differentially? Or what do you suggest?

Thank you again

Oselm

[Gabriel Landini]

On Friday 10 Jul 2015 07:38:39 oselm wrote:
> The main problem now is to find a way to threshold the picture. In
> particular, the yellow of the eggs is not homogenous across the picture and
> therefore it is not possible to distinguish between eggs in pale yellow and
> the spots between eggs in the agglomerate (also colored in pale yellow). Is
> there a way to threshold different zone of the picture differentially? Or
> what do you suggest?

You need better illumination (to minimise shadow) AND a different (more
contrasting, black?) background colour.

Cheers

Gabriel

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