xylem cell area measuring

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xylem cell area measuring

yossi
Hi
I need to measure and count xylem cells in cross sections of plant.
how can I do this?
I add a picture before I do nothing to it, and after I clean it so that just
what I want to measure stay there.
Thank you!
Yossi


<http://imagej.1557.x6.nabble.com/file/t382477/B_186_3%2C4_before.png>
<http://imagej.1557.x6.nabble.com/file/t382477/B_186_3%2C4_after.png>




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Re: xylem cell area measuring

Straub, Volko A. (Dr.)
Hi Yossi,

I would suggest you have a look at the 'Analyze Particles' command (https://imagej.net/Particle_Analysis#Analyze_Particles) or the 'Extended Particle Analyzer' (part of the BioVoxxel toolbox; https://imagej.net/BioVoxxel_Toolbox), which should be able to do what you want on the thresholded images.

Hope this helps,
Volko

-----Original Message-----
From: yossi <[hidden email]>
Sent: 03 December 2019 11:22
To: [hidden email]
Subject: xylem cell area measuring

Hi
I need to measure and count xylem cells in cross sections of plant.
how can I do this?
I add a picture before I do nothing to it, and after I clean it so that just what I want to measure stay there.
Thank you!
Yossi


<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.1557.x6.nabble.com%2Ffile%2Ft382477%2FB_186_3%252C4_before.png&amp;data=02%7C01%7Cvs64%40leicester.ac.uk%7C67441a5cd98045e1bbd208d777e54815%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637109698952207140&amp;sdata=v6kPokP01glo5D5MxGpIymyU7WDtN%2BbY8xvYsf9Unx4%3D&amp;reserved=0>
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Re: xylem cell area measuring

yossi
In reply to this post by yossi
The 'analyse particle' is working good after I work very hard to clean the picture, but I hope to find an way to do so without cleaning at all. even if there is a way to clean most of it by some automatic way, it will save me ton's of time.
Yossi

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Re: xylem cell area measuring

yossi
In reply to this post by yossi
Hi again!

I try to use the 'extended particle analyzer', but it not working...
I atacched the picture after 'make binary', and the outlines after the analyzer.
what is wrong?

Thank's,
Yossi


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‏‏לכידה2.PNG (272K) Download Attachment
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Re: xylem cell area measuring

Straub, Volko A. (Dr.)
Hi Yossi,

I am not 100% sure what you try to measure, but I assume that you are interested in the black, round/oval structures on your image.
The Particle Analyzer/Enhanced Particle Analyzer detects white particles on a black background. So, you need to invert your image. After converting your jpg image to a binary b/w image and inverting it, using the Particle Analyzer with a size limit of 10-infinty and a circularity limit of 0.50-1.00 detects 608 structures (see attached images).
Is this roughly what you had in mind?

Cheers,
Volko



-----Original Message-----
From: ImageJ Interest Group <[hidden email]> On Behalf Of Yossi
Sent: 04 December 2019 08:27
To: [hidden email]
Subject: Re: xylem cell area measuring

Hi again!

I try to use the 'extended particle analyzer', but it not working...
I atacched the picture after 'make binary', and the outlines after the analyzer.
what is wrong?

Thank's,
Yossi
 

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Re: xylem cell area measuring

yossi
In reply to this post by yossi
Hi Volko!

It's seems to go in the right direction, but I need to check it by my self.
how you convert it from black to white?

Yossi

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Re: xylem cell area measuring

Straub, Volko A. (Dr.)
To invert an image, use 'Edit'->'Invert'.

Good luck,
Volko


-----Original Message-----
From: ImageJ Interest Group <[hidden email]> On Behalf Of Yossi
Sent: 04 December 2019 14:15
To: [hidden email]
Subject: Re: xylem cell area measuring

Hi Volko!

It's seems to go in the right direction, but I need to check it by my self.
how you convert it from black to white?

Yossi

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