how to measure the total length of a segments network ?

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
8 messages Options
Reply | Threaded
Open this post in threaded view
|

how to measure the total length of a segments network ?

vitistgo
Hi everyone :)

I've been looking for days for a method to measure the cumulative length of different veins on leaves pictures, but without result... so i'm asking for a bit of help from more experimented people than me in ImageJ :p
Here is one of the pictures that I have to analyze :


The idea is to know the cumulative length of every vein (each little segment), but without having to mark each one of them. I already tried to threshold the picture so that only the veins appear clearly, but then i don't know if there is like an "automated function" to recognize all the segments and summarize their total length... Is there ? :)

Thanks for helping !

Reply | Threaded
Open this post in threaded view
|

Re: how to measure the total length of a segments network ?

fabrice senger-2
Hi,

if you're happy with the result of your segmentation you might use
"skeleton" and "analyze skeleton" built in in FIJI.
You will even get stats out of your image ...

Cheers,

Fabrice.

2016-07-11 17:20 GMT+02:00 vitistgo <[hidden email]>:

> Hi everyone :)
>
> I've been looking for days for a method to measure the cumulative length of
> different veins on leaves pictures, but without result... so i'm asking for
> a bit of help from more experimented people than me in ImageJ :p
> Here is one of the pictures that I have to analyze :
> <http://imagej.1557.x6.nabble.com/file/n5016851/P1050025.jpg>
>
> The idea is to know the cumulative length of every vein (each little
> segment), but without having to mark each one of them. I already tried to
> threshold the picture so that only the veins appear clearly, but then i
> don't know if there is like an "automated function" to recognize all the
> segments and summarize their total length... Is there ? :)
>
> Thanks for helping !
>
>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/how-to-measure-the-total-length-of-a-segments-network-tp5016851.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: how to measure the total length of a segments network ?

vitistgo
Hi Fabrice :)

That sounds perfect indeed, but what's FIJI and where can I find it ?

Cheers,

Camille.
Reply | Threaded
Open this post in threaded view
|

Re: how to measure the total length of a segments network ?

fabrice senger-2
search for "FIJI , ImageJ" and you will get the answers.

Have fun,

Fabrice.

2016-07-11 17:48 GMT+02:00 vitistgo <[hidden email]>:

> Hi Fabrice :)
>
> That sounds perfect indeed, but what's FIJI and where can I find it ?
>
> Cheers,
>
> Camille.
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/how-to-measure-the-total-length-of-a-segments-network-tp5016851p5016854.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: how to measure the total length of a segments network ?

shelleyu
In reply to this post by fabrice senger-2
Hello,

I am also trying to measure the total length of multiple lines in one image.
Skeleton does not work as it picks up the cell lines and not just the veins
:(

Is there any other way? It would be great even if you could just edit
'summarise' to include a total instead of just mean,mode etc

Otherwise I have to copy all the numbers out of image j results into excel,
add them together then transfer that value to my actual results spreadsheet.
This gets tedious when there are hundreds of images to get through :(

Thank you for any wisdom in advance!!




--
Sent from: http://imagej.1557.x6.nabble.com/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: how to measure the total length of a segments network ?

Straub, Volko A. (Dr.)
Difficult to provide any advice without some more detail on what you are actually trying to measure. A sample image would be useful. If you try to measure linear structures, but avoid circular structures, you might need to do some shape filtering, which can easily be achieved using e.g. the Extended Particle Analyzer.
Hope this helps.
Volko

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of shelleyu
Sent: 28 February 2018 04:51
To: [hidden email]
Subject: Re: how to measure the total length of a segments network ?

Hello,

I am also trying to measure the total length of multiple lines in one image.
Skeleton does not work as it picks up the cell lines and not just the veins :(

Is there any other way? It would be great even if you could just edit 'summarise' to include a total instead of just mean,mode etc

Otherwise I have to copy all the numbers out of image j results into excel, add them together then transfer that value to my actual results spreadsheet.
This gets tedious when there are hundreds of images to get through :(

Thank you for any wisdom in advance!!




--
Sent from: http://imagej.1557.x6.nabble.com/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: how to measure the total length of a segments network ?

heliguy
Hello
I hope its ok to jump in here, as i have similar request.

I am trying to measure the length of the streams (pencil lines) in this
image.
I would need to trace over the lines, as I need to measure in groups to get
total length of first order, second order and so on.
To achieve this I could trace out a series of small segments and then get a
total length, rinse and repeat.
Is this possible with imagej or should i look elsewhere?
  <http://imagej.1557.x6.nabble.com/file/t381937/Water_catchment_area.jpg>



--
Sent from: http://imagej.1557.x6.nabble.com/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: how to measure the total length of a segments network ?

Straatman, Kees (Dr.)
Dear Heliguy,

I think It should be possible to get this information using ImageJ, however the image provided is not a clean image as it shows also parts/lines from the map under it. This makes it difficult to extract the drawn line structures.

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
www.le.ac.uk/advanced-imaging-facility
-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of heliguy
Sent: 28 February 2018 14:05
To: [hidden email]
Subject: Re: how to measure the total length of a segments network ?

Hello
I hope its ok to jump in here, as i have similar request.

I am trying to measure the length of the streams (pencil lines) in this image.
I would need to trace over the lines, as I need to measure in groups to get total length of first order, second order and so on.
To achieve this I could trace out a series of small segments and then get a total length, rinse and repeat.
Is this possible with imagej or should i look elsewhere?
  <http://imagej.1557.x6.nabble.com/file/t381937/Water_catchment_area.jpg>



--
Sent from: http://imagej.1557.x6.nabble.com/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html