http://imagej.273.s1.nabble.com/thresholding-and-detection-issues-when-analyzing-particles-to-obtain-object-counts-in-a-petri-dish-tp5015178p5015188.html
image formats than JPEG. In any case have a look at the scanner-manual
of the dish, i.e. one that results in good contrast of the eggs (little
stray light) without reflections. You may also experiment with color
The settings of the camera are of utmost importance. If possible use the
depth of focus] and exposure times). Don't use the flash.
> Thanks Herbie and Aryeh. Unfortunately, we are scanner limited (and only
> saves a jpeg) and do not currently have funding for this project to buy one
> suited for higher quality images. I did reduce the size of the images I
> sent to be able to fit in emails but agree they still lack optimal
> 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
> of any free programs that would give me this option? Thanks again for
> everyone input.
>
> 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