noisy. You may have to smooth it before thresholding.
> 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.html>
> Load 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