http://imagej.273.s1.nabble.com/thresholding-and-detection-issues-when-analyzing-particles-to-obtain-object-counts-in-a-petri-dish-tp5015178p5015198.html
want (*.pnm for no-compressed image for example). If you need more
> Rich,
>
> I doubt that a scanner needs another software in order to output other
> image formats than JPEG. In any case have a look at the scanner-manual
> that will tell you about its optical resolution as well.
>
> What you could try is use a digital camera but one that
> 1.
> is able to output uncompressed raw-images
> 2.
> has decent optics that give you good image quality for the given
> object distance.
>
> If you can find and use such a camera, then try for optimum
> illumination 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 filters.
>
> The settings of the camera are of utmost importance. If possible use
> the "gamma = 1" mode, deselect all preprocessing options, such as
> sharpening (contrast enhancement), and don't use a high
> ASA-sensitivity setting (just one that fits your illumination at
> reasonable stops [watch for the depth of focus] and exposure times).
> Don't use the flash.
>
> HTH
>
> Herbie
>
> ::::::::::::::::::::::::::::::::::::::::::::
> Am 09.12.15 um 16:42 schrieb Rich Pendleton:
>> 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
>
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