Re: thresholding and detection issues when analyzing particles to obtain object counts in a petri dish

Posted by Rich Pendleton on Dec 09, 2015; 1:39pm
URL: http://imagej.273.s1.nabble.com/thresholding-and-detection-issues-when-analyzing-particles-to-obtain-object-counts-in-a-petri-dish-tp5015178p5015183.html

Thank you Ben and Aryeh.  At this point, total egg counts is the main
objective, but eventually we would like to use the area and perimeter
information from analyze particles to estimate egg size.  Do you have any
additional information that could lead to me still utilizing the analyze
particles function?

Thanks again,

Rich

On Tue, Dec 8, 2015 at 11:28 PM, Aryeh Weiss <[hidden email]> wrote:

> On 08/12/2015 10:57 PM, Rich Pendleton wrote:
>
>> Hey all,
>>
>>
>>
>> I was wondering if someone might be able to provide some insight similar
>> to
>> a question that was posted last month.  I am trying to use the analyze
>> particles function to count fish eggs in a petri dish.  Some eggs are more
>> mature than others and the smaller less mature eggs are rather
>> transparent.  Therefore when trying to adjust the threshold to detect the
>> less mature eggs, I get clumping of mature eggs that are in close
>> proximity
>> to one another.  Despite using the watershed function in attempt to
>> separate eggs that are close, I still have many large clumps that have
>> numerous eggs that are being counted as one unit. As a result, the counts
>> are always much less than the true count (often over 1000 eggs less). If I
>> adjust the threshold in the other direction, I am unable to detect the
>> less
>> mature eggs.  It is quite difficult to prevent eggs from clumping when the
>> petri dish is first scanned therefore was hoping I might be able to get
>> around it within ImageJ. I have attached a few pictures (from top to
>> bottom) 1) original image set to 8 bit, 2) after thresholding, 3) after
>> watershed, 4) outlines of counted particles.  The original image was
>> scanned in as a jpeg with 1200 dpi.  Any help that you may be able to
>> provide would be greatly appreciated.
>>
>>
> Try Process>Find Maxima..
> For your image, a threshold of about 15 seems to work.
> Process>Subtract Background may also help if you want to threshold, but I
> dont think Find Maxima needs it.
>
> However, I suggest that you not acquire your images as jpg -- use a format
> that is not lossy ( or acquire uncompressed).
> You resolution is currently about 20 micron/dot (1200 dots in 25.4 mm).
> You might do better if you can get a higher resolution scan.
>
> --aryeh
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: [phone]
>
>

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