http://imagej.273.s1.nabble.com/thresholding-and-detection-issues-when-analyzing-particles-to-obtain-object-counts-in-a-petri-dish-tp5015178p5015187.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
> 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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