Posted by
ali ayata on
Jun 12, 2008; 7:57pm
URL: http://imagej.273.s1.nabble.com/Shadow-problem-tp3695874p3695880.html
i don't know it would be helpfull, but have suggestions about capturing. (if it would be possible to recapture your work..)
using indirect sunlight during photography would be maintain homogenous illuminated image.
you can also use backlight illumination with a horizontally placed negatoscope (x ray film viewer). it would be prevent shading.
or do not place the petri on a surface, try to hold it in the air by fixing form its edge.
i hope it would be helpful ...
ali ayata
istanbul
--- On Thu, 6/12/08, Kashif Zeeshan <
[hidden email]> wrote:
From: Kashif Zeeshan <
[hidden email]>
Subject: Re: Shadow problem
To:
[hidden email]
Date: Thursday, June 12, 2008, 1:22 PM
Hi,
Thanks a lot for your response. I am sending you the link of my 3 photos
where I want to do the image analysis.
http://s305.photobucket.com/albums/nn227/ablaze212/In fact, I want to count the aggregates (or particles) present in the Petri
dishes. My objective is to quantify their total number, their area, diameter
and density.
I hope I was able to explain the situation.
Thanks again. Meanwhile I am trying to do as you said.
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
-----Message d'origine-----
De : ImageJ Interest Group [mailto:
[hidden email]] De la part de David
Randell
Envoyé : jeudi 12 juin 2008 18:45
À :
[hidden email]
Objet : Re: Shadow problem
On Thursday 12 June 2008 14:01:30 Kashif Zeeshan wrote:
> Hi,
>
> Thanks for your nice suggestions. Actually, I am totally new to ImageJ and
> up to now it seems me very difficult to use this. Can you kindly tell me
> from where to start? The images I am using are colored imaged taken
through
> an ordinary camera (5M pixels) in the neon light. The liquid medium
> containing aggregates was being poured in a large Petri dish and then the
> photos were being taken from the above. To avoid the reflection of the
> light and camera, I placed the Petri dishes in a corner of a room but due
> to this now I have the shadows in the images. With the help of the replies
> of this group experts, I was able to do some analysis. But ImageJ count
> these shadows either as a part of the aggregates or separate aggregates. I
> read the paper sent in the previous email. Thanks again for this help. But
> where I will find this option of HSV color-space? I am sorry that most of
> the times these terms given by the experts are difficult also and I am not
> able to understand all. Can you kindly help me to sort out the problem?
> Where I can find this option or how can I do this please?
There are several colour space related plugins one can use with ImageJ. I
would suggest you look up and install the Threshold_colour plugin by Gabriel
Landini:
http://www.dentistry.bham.ac.uk/landinig/software/software.htmlLoad the colour image into ImageJ and select the threshold option from the
main menu bar (the icon looks like the moon at last quarter). This will open
up a window with a set of slider bars where for the HSB option (same as HSV)
you can change the Hue, Saturation and Brightness (or Hue, Saturation and
Value for HSV). This will give you some idea of what can be done by
manipulating these channels. There are other options in ImageJ where you can
convert a colour image into a HSV stack (3 images: one for each channel),
and
then extract each one in turn. If the manual manipulation of the image
works,
then depending on how many images you need to process, it may be time to
consider writing a macro to process these. For this read the Help file
associated with this plugin.
Without seeing an example image and you being a bit clearer what you want to
segment out of your images, its a bit difficult to say much more than this
at
this stage.
Best regards,
Dave Randell