Re: Image analysis of aggregates in a liquid medium

Posted by GCH-2 on May 06, 2008; 3:59pm
URL: http://imagej.273.s1.nabble.com/Image-analysis-of-aggregates-in-a-liquid-medium-tp3696326p3696327.html

Kashif,

Since you are having problems with the reflection I assume that the  
range of greylevels (colors) varies between the images. You may want  
to try the IJ/Process/FFT/ Bandpass filter... to keep the structures  
corresponding to the aggregates. Use an upper limit corresponding to  
approx. the size of the aggregates. Threshold after the bandpass  
filtering.

Isnt possible to scan the images in a desktop scanner instead of  
using a camera?. Scanners are good and stable devices for this  
purpose and if you have the aggregates in a liquid transparent  
medium, it shouldnt be a problem. How big are the aggregates? Play a  
bit with reflection and transmission mode.

I hope this helps,

Gary.
http://www.gcsca.net


On May 6, 2008, at 4:06 PM, Kashif Zeeshan wrote:

> HI,
>
>
>
> I am a new user of ImageJ (I am using MacBiophotonic ImageJ  
> upgraded to
> version 1.41a) and I am trying to practice the image analysis to  
> quantify
> the aggregates present in liquid medium. But I am facing a lot of  
> problems.
> Sometimes, the threshold it works and sometimes it doesn’t. I try  
> to explain
> a little bit the procedure. I pour the medium with aggregates into  
> a large
> Petri dish and then I take photo with a dark blue background by an  
> ordinary
> digital camera (Panasonic, DMC-LS2, 5 Mega Pixels) in default mode  
> without
> flash. I have a problem of reflection of light. After taking photos, I
> transfer them to the computer and launch ImageJ. In ImageJ, I open the
> selected image and then I use the toolbar button “RGB-Merge/Split”  
> to have
> the 3 different images (transferred into red, blue and green. I  
> keep the red
> one for further processing. On that red image, I apply the  
> Segmentation
> plugin “Otsu Thresholding 8bit”. After that I use the command
> Analyze>Analyze Particles… . It worked for one assay but not  
> working now. I
> am blocked at this stage. Can you kindly give me some suggestion to  
> improve
> the methodology or how I can progress with this?
>
>
>
> Cordially.
>
>
>
> Kashif ZEESHAN
>
> (00 33 6 74 90 18 10)
>
> Doctorant, Biopesticide Group,
>
> Laboratoire Universitaire de
>
> Biodiversité et d'Ecologie
>
> Microbienne (LUBEM),
>
> 6 Rue de l'Université,
>
> 29334, Quimper Cedex,
>
> France
>
>