Re: thresholding and detection issues when analyzing particles to obtain object counts in a petri dish
Posted by
Aryeh Weiss on
Dec 09, 2015; 5:28am
URL: http://imagej.273.s1.nabble.com/thresholding-and-detection-issues-when-analyzing-particles-to-obtain-object-counts-in-a-petri-dish-tp5015178p5015180.html
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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