Question about Mice Axon Count using ImageJ

[succinator]

Hello, everyone. This is Steven. Right now I am working on quantification of axon in mice model. I am trying to figure out an efficient way to quantify my samples. I tried
1st:using threshold(black and white), in this step some of the axon detail was lost, some area is either too white or black, how could I avoid this, is there a way to locally treating the contrast
2nd:using nucleus count, this step was not really efficient, I am still trying to improve the count as it counts much less than what is out there
This is basically what I have done, I am willing to listen to any suggestions or other methods to quantify. Thanks, and I attached one of the image that I took to give an example to what I am working on.
http://postimage.org/image/z5jronpy9/

[Albert Cardona-2]

2012/9/29 succinator <[hidden email]>:

> Hello, everyone. This is Steven. Right now I am working on quantification of
> axon in mice model. I am trying to figure out an efficient way to quantify
> my samples. I tried
> 1st:using threshold(black and white), in this step some of the axon detail
> was lost, some area is either too white or black, how could I avoid this, is
> there a way to locally treating the contrast
> 2nd:using nucleus count, this step was not really efficient, I am still
> trying to improve the count as it counts much less than what is out there
> This is basically what I have done, I am willing to listen to any
> suggestions or other methods to quantify. Thanks, and I attached one of the
> image that I took to give an example to what I am working on.
> http://postimage.org/image/z5jronpy9/
> <http://postimage.org/image/z5jronpy9/>
>

You could first normalize the image with CLAHE.
Then you could do the object detection by using Plugins - Segmentation
- Trainable Segmentation (it's like a fancy threshold). After
obtaining the mask, run the Particle Analyzer on it to count elements.

Both plugins are pre-installed in Fiji (http://fiji.sc).

Albert

--
http://albert.rierol.net
http://www.ini.uzh.ch/~acardona/

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[Judith]

Hi, everyone,  

This is Judith, I'm working on quantification of axon in rabbit model. I am trying to figure out an efficient way to quantify my samples with AxonJ, although it doesn't work:  I tried

1st: normalize the image with CLAHE.
2nd: using adjust--color threshold(black and white),
3rd: Pluggin AxonJ and it doesn't work (unrecognized command as CLAHE , and FeatureJ Hessian)

When I change step 3 in Fiji  just to Analize Particles, it seems Is working the axon counting but I'd like to use  AxonJ  tool in the right way.
I am willing to listen to any suggestions

Thanks in advance,
Judith