Particle Analysis

[Florian Sedlmeir]

Hi,

I want to analyse particle-like structures with ImageJ. The problem is,  
that these particles usually have a good contrast against their local  
environment, but globally there are too many areas with similar or same  
grey values to threshold the image. So i have a few questions concerning  
this:

- Is there an easy way to threshold only selected areas in a picture (to  
threshold the whole picture step by step)?

- My particles are easily distinguishable with the eye because they are  
not as rough as their environment (+usually  there is a local difference  
in contrast). ImageJ is able to find the edges with the "find edges" tool,  
but unfortunatly it doesn´t create closed areas (my plan was to find  
edges, threshold the resulting picture and analyse the resulting particles  
then) Is there a solution for this a problem?

- One of my friends showed me the "magic wand" tool in Photoshop, which is  
able to determine my particles properly. Unfortunatly the same tool in  
ImageJ is not able to do this, it seems to be too sensitive. (Are there  
parameters which can be adjustet?)
So my question is: Does a plugin exist, which is able to do the same task  
as Photoshop´s magic wand?


Thank you and best regards.
Florian

[Stoyan Pavlov]

Hi Florian,
Clicking twice on the magic wand icon brings up a window for configuration.

Best regards

Stoyan Pavlov
On Thu, Nov 26, 2009 at 1:17 PM, Florian Sedlmeir
<[hidden email]> wrote:

> Hi,
>
> I want to analyse particle-like structures with ImageJ. The problem is, that
> these particles usually have a good contrast against their local
> environment, but globally there are too many areas with similar or same grey
> values to threshold the image. So i have a few questions concerning this:
>
> - Is there an easy way to threshold only selected areas in a picture (to
> threshold the whole picture step by step)?
>
> - My particles are easily distinguishable with the eye because they are not
> as rough as their environment (+usually  there is a local difference in
> contrast). ImageJ is able to find the edges with the "find edges" tool, but
> unfortunatly it doesn´t create closed areas (my plan was to find edges,
> threshold the resulting picture and analyse the resulting particles then) Is
> there a solution for this a problem?
>
> - One of my friends showed me the "magic wand" tool in Photoshop, which is
> able to determine my particles properly. Unfortunatly the same tool in
> ImageJ is not able to do this, it seems to be too sensitive. (Are there
> parameters which can be adjustet?)
> So my question is: Does a plugin exist, which is able to do the same task as
> Photoshop´s magic wand?
>
>
> Thank you and best regards.
> Florian
>

--
Dr. Stoyan P. Pavlov, MD
Departament of Anatomy, Histology and Embryology
Medical University "Prof. Dr. Paraskev Stoyanov", Varna
Prof. Marin Drinov Str.55
9002 Varna
 Bulgaria
Tel: +359 (0) 52 - 677 - 050 #2638
e-mail: [hidden email]

[Michael Schmid]

Hi Florian,

a few more ideas:

- use Process>Subtract background

- try the Versatile Wand from the documentation wiki with a gradient  
threshold. You could click on the background, then invert the  
selection, so you have all particles.
   http://imagejdocu.tudor.lu/doku.php?
id=plugin:segmentation:versatile_wand:start

- if the background is rough everywhere, run  
Process>Filters>Variance, then do some smoothing (maybe edge-
preserving, e.g. Sigma Blur from the ImageJ site or Thresholded Blur  
from the documentation wiki). Maybe you can threshold this image more  
easily.


Michael
________________________________________________________________

On 26 Nov 2009, at 12:17, Florian Sedlmeir wrote:

> Hi,
>
> I want to analyse particle-like structures with ImageJ. The problem  
> is, that these particles usually have a good contrast against their  
> local environment, but globally there are too many areas with  
> similar or same grey values to threshold the image. So i have a few  
> questions concerning this:
>
> - Is there an easy way to threshold only selected areas in a  
> picture (to threshold the whole picture step by step)?
>
> - My particles are easily distinguishable with the eye because they  
> are not as rough as their environment (+usually  there is a local  
> difference in contrast). ImageJ is able to find the edges with the  
> "find edges" tool, but unfortunatly it doesn´t create closed areas  
> (my plan was to find edges, threshold the resulting picture and  
> analyse the resulting particles then) Is there a solution for this  
> a problem?
>
> - One of my friends showed me the "magic wand" tool in Photoshop,  
> which is able to determine my particles properly. Unfortunatly the  
> same tool in ImageJ is not able to do this, it seems to be too  
> sensitive. (Are there parameters which can be adjustet?)
> So my question is: Does a plugin exist, which is able to do the  
> same task as Photoshop´s magic wand?
>
>
> Thank you and best regards.
> Florian

[dpoburko]

I had a similar problem so I wrote a macro to run multiple thresholds
based on user defined variables. I believe there are similar macros out
there, but this one works well for me. I've hesitated making it
available to the whole community for lack of polish. But you're welcome
to give it a try. The idea is that it will determine the max intensity
in your image, perform a series of thresholds. It then uses analyze
particles for each threshold. As defined particles grow, the macro will
stop counting a given particle when it hits a maximum size. This allows
it to find small particles of greatly varying intensity of local
background.

Anyhow, let me know if you would like to give it a try and I'll clean up
the code to make it more self-explanatory.

Cheers,
Damon


Florian Sedlmeir wrote:

> Hi,
>
> I want to analyse particle-like structures with ImageJ. The problem
> is, that these particles usually have a good contrast against their
> local environment, but globally there are too many areas with similar
> or same grey values to threshold the image. So i have a few questions
> concerning this:
>
> - Is there an easy way to threshold only selected areas in a picture
> (to threshold the whole picture step by step)?
>
> - My particles are easily distinguishable with the eye because they
> are not as rough as their environment (+usually  there is a local
> difference in contrast). ImageJ is able to find the edges with the
> "find edges" tool, but unfortunatly it doesn´t create closed areas (my
> plan was to find edges, threshold the resulting picture and analyse
> the resulting particles then) Is there a solution for this a problem?
>
> - One of my friends showed me the "magic wand" tool in Photoshop,
> which is able to determine my particles properly. Unfortunatly the
> same tool in ImageJ is not able to do this, it seems to be too
> sensitive. (Are there parameters which can be adjustet?)
> So my question is: Does a plugin exist, which is able to do the same
> task as Photoshop´s magic wand?
>
>
> Thank you and best regards.
> Florian

[Gabriel Landini]

> I want to analyse particle-like structures with ImageJ. The problem
> is, that these particles usually have a good contrast against their
> local environment, but globally there are too many areas with similar
> or same grey values to threshold the image.

You should try the new CLAHE plugin (see IJ or Fiji sites), and/or the local
thresholding methods.

The latter jar for IJ can be found here:
http://www.dentistry.bham.ac.uk/landinig/software/autothreshold/autothreshold.html
and it is by default included in Fiji.

Cheers.

G.