Posted by
Michael Schmid on
Oct 30, 2008; 12:04pm
URL: http://imagej.273.s1.nabble.com/Thresholding-help-tp3694620p3694624.html
Hi Justin,
the ImageJ built-in "subtract background" command should work well
with your type of image.
It will be very difficult to extract the weakly visible sides of the
particles. For a rough size estimate of the circular particles, a way
out might be checking the width of the rectangular bounding box and
Feret's diameter - if these sizes agree within reasonable limits,
they shuld be ok. For the remaining particles you have to do it
manually.
Here is a macro for the first steps:
run("32-bit");
run("Smooth");
run("Subtract Background...", "rolling=100 light sliding");
setThreshold(-9999, -10);
run("Set Measurements...", " bounding feret's redirect=None
decimal=3");
run("Analyze Particles...", "size=10-Infinity
circularity=0.00-1.00 show=[Nothing] display include record");
If this is not enough, you need either better illumination or a
plugin that fits full circles into the arcs (I am not aware of any,
you might have to write it yourself).
Michael
________________________________________________________________
Michael Schmid email:
[hidden email]
Institut fuer Allgemeine Physik, Technische Universitaet Wien
Wiedner Hauptstr. 8-10/134, A 1040 Wien, Austria
Tel. +43 1 58801-13452 or -13453, Fax +43 1 58801 13499
________________________________________________________________
On 29 Oct 2008, at 22:02, Michael Doube wrote:
> Justin:
>
> How about subtracting the background gradient from the image to
> improve contrast?
>
> Just take a 'background' image without any droplets and use Process-
> >Image Calculator, subtracting your background from the droplets
> +background image. I had a quick go on your example and greatly
> improved the ability to discriminate the droplet contours.
>
> Mike
>
> Fabrice Senger wrote:
>> Quoting Justin Walker <
[hidden email]>:
>>> I have a series of images of liquid droplets, which have very poor
>>> contrast with the surrounding phase, due to the similarities in
>>> their
>>> index of refraction. I get enough contrast in my images to
>>> clearly see
>>> the droplets, however, I can't pick them out with the threshold
>>> because
>>> there is a slight gradient in the brightness of my lighting.
>>> Link to a
>>> sample image is below:
>>>
>>>
http://www.chejrw.com/forum/test.tif>>>
>>> Does anyone know of a way I can manipulate this image to be able
>>> to use
>>> the 'measure particles' plugin to get the droplet sizes? I can
>>> clearly
>>> see the droplets, so surely there must be a way to make the computer
>>> see them.
>>>
>>> Thanks everybody
>>>
>>> - Justin Walker
>> As far I can see in your images, you can see the "contour" of the
>> droplets.
>> If you invert your image, this "contour" should appear bright in a
>> dark background.
>> This should help.
>> Fabrice.