Posted by
Aryeh Weiss on
Dec 09, 2015; 2:31pm
URL: http://imagej.273.s1.nabble.com/thresholding-and-detection-issues-when-analyzing-particles-to-obtain-object-counts-in-a-petri-dish-tp5015178p5015185.html
On 09/12/2015 3:39 PM, Rich Pendleton wrote:
> 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?
>
The find maxima command has a segmentation option that segments your
image into regions, each (hopefully) with a single object.
Also, after doing background subtraction, you might try hysteresis
segmentation.
You can find this in the 3D ImageJ Suite
http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:startThey have a Fiji update site.
This allows you to set a low enough threshold that you can include the
entire egg, but only if the object includes a peak higher than the upper
threshold.
I think you will really need higher resolution. I do not know what
constraints you have, but there are scanners
with 6400 DPI optical resolution and even higher, so that you can get
more than a few pixels across the eggs.
Best regards
--aryeh
> Thanks again,
>
> Rich
>
> On Tue, Dec 8, 2015 at 11:28 PM, Aryeh Weiss <
[hidden email]
> <mailto:
[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
>
>
--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel
Ph: 972-3-5317638
FAX: 972-3-7384051
--
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