Image analysis of aggregates in a liquid medium

[Kashif Zeeshan]

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

 

[GCH-2]

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
>
>