http://imagej.273.s1.nabble.com/thresholding-and-detection-issues-when-analyzing-particles-to-obtain-object-counts-in-a-petri-dish-tp5015178p5015189.html
> Thanks Herbie and Aryeh. Unfortunately, we are scanner limited (and only
> suited for higher quality images. I did reduce the size of the images I
> resolution. I know you can use other programs such as photoshop to run a
> scanner with options other than the scanner's default options. Do you know
> On Wed, Dec 9, 2015 at 9:16 AM, Herbie <
[hidden email]> wrote:
>
>> Rich,
>>
>> as others have pointed out already, the spatial resolution of the shown
>> image is generally _too small_, and especially if you
>> "would like to use the area and perimeter information from analyze
>> particles to estimate egg size."
>>
>> Maybe scans of parts of your dish may help but this depends on the optics
>> of your scanner.
>>
>> Please note that it is important to consider the _optical_ resolution of
>> scanners. (Interpolated resolution is for selling not for science.)
>>
>> Again, don't use compressed image formats! In case your scanner outputs
>> JPEG-images only, then it is _not_ suited for scientific purposes.
>>
>> Have success
>>
>> Herbie
>>
>> ::::::::::::::::::::::::::::::::::::::::::::
>> Am 09.12.15 um 14:39 schrieb Rich Pendleton:
>>
>> 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: 972-3-7384051
>>>>
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