How to measure Directness or Straightness of processes of neurons?

classic Classic list List threaded Threaded
6 messages Options
Reply | Threaded
Open this post in threaded view
|

How to measure Directness or Straightness of processes of neurons?

avarone
I'm going crazy, I would like to find a way to measure the directness or how
straight the lines drawn on imagej are (see image attached). Does anyone
know how to do it?

Many thanks in advance,

Anna

<http://imagej.1557.x6.nabble.com/file/t382123/imagej_directness_question.png>



--
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 Directness or Straightness of processes of neurons?

Robert Vannucci
I would think that you would have no problem tracing the axon with the
freehand line tool.  It might take a little practice.
If you have a Mac without a right hand click, you can select the freehand
line tool from the straight line by holding down the Control key.
Then select.
PS.  This is my first response to a question regarding Imagej.  It should
be fun
Bob Vannucci at FAU and Weil Cornell.

On Tue, Oct 2, 2018 at 3:02 PM avarone <[hidden email]> wrote:

> I'm going crazy, I would like to find a way to measure the directness or
> how
> straight the lines drawn on imagej are (see image attached). Does anyone
> know how to do it?
>
> Many thanks in advance,
>
> Anna
>
> <
> http://imagej.1557.x6.nabble.com/file/t382123/imagej_directness_question.png>
>
>
>
>
> --
> 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 Directness or Straightness of processes of neurons?

Straub, Volko A. (Dr.)
In reply to this post by avarone
Hi Anna,


Not quite sure what sort of measure you are looking for. But you could measure the length of the line that you have drawn and then also calculate the distance between the two endpoints of your line. The ratio of the two measurements could be taken as a measure of straightness with a completely straight line having a ratio of 1.


Hope this helps,

Volko

________________________________
From: avarone <[hidden email]>
Sent: 02 October 2018 19:50:49
To: [hidden email]
Subject: How to measure Directness or Straightness of processes of neurons?

I'm going crazy, I would like to find a way to measure the directness or how
straight the lines drawn on imagej are (see image attached). Does anyone
know how to do it?

Many thanks in advance,

Anna

<http://imagej.1557.x6.nabble.com/file/t382123/imagej_directness_question.png>



--
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 Directness or Straightness of processes of neurons?

Andrew-2
In reply to this post by avarone
Anna,

I think you are looking for the tortuosity of the line (as a guess). Volko
is right, but there is a plugin to do this: The analyze skeleton plugin (
https://imagej.net/AnalyzeSkeleton) can determine the branch length and
euclidean distance, which combined I believe can give an indication of the
tortuosity (though from what I gather there are better ways to quantify
this, but they are not available in ImageJ).


Andrew

On Tue, Oct 2, 2018 at 3:02 PM avarone <[hidden email]> wrote:

> I'm going crazy, I would like to find a way to measure the directness or
> how
> straight the lines drawn on imagej are (see image attached). Does anyone
> know how to do it?
>
> Many thanks in advance,
>
> Anna
>
> <
> http://imagej.1557.x6.nabble.com/file/t382123/imagej_directness_question.png>
>
>
>
>
> --
> 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 Directness or Straightness of processes of neurons?

Rainbow
Hi Volko,

Thanks for sharing your idea! For the time being, I am working on the
calculation of Euclidean distance between two endpoints of a curved line.
This line is selected in ROIs Manager. Could you please explain more about
how to measure the distance between the endpoints?

Best wishes,

Yuhong



--
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 Directness or Straightness of processes of neurons?

Straub, Volko A. (Dr.)
Dear Yuhong,

Sorry for the delay in responding to your query, but I have been away.
If you have a b/w image with white lines on a black background (e.g. by creating a skeleton of a thresholded image)  the easiest way to calculate the Euclidean distance between the endpoints of the lines as well as the total length of the line path is probably to use the 'Analyze Skeleton (2D/3D)' function in ImageJ (Analyze->Skeleton->Analyze Skeleton (2D/3D). If you tick the option to 'Show detailed information', it produces a table that shows the branch length, end point coordinates, Euclidean distance between end points of branches, etc.
Below is a short macro that creates two polylines that cross each other and then uses the 'Analyse Skeleton' function to show the information for each of the 5 non-crossing segments. It also shows a tagged image that colour codes the pixels of the skeleton to indicate end points, junctions and crossings.
In order to measure the length of a specific ROI selected in the ROI manager, I would probably copy the ROI to an empty image and then use the 'Analyse Skeleton' function.

I hope this helps to answer your question,
Volko

newImage("Test", "8-bit black", 200, 200, 1);
makeLine(34,92,60,70,91,81,115,35,159,96,130,120,168,121);
run("Draw", "slice");
makeLine(83,26,145,23,159,49,130,120);
run("Draw", "slice");
run("Analyze Skeleton (2D/3D)", "prune=none show display");


________________________________
From: Rainbow <[hidden email]>
Sent: 16 July 2019 21:29
To: [hidden email] <[hidden email]>
Subject: Re: How to measure Directness or Straightness of processes of neurons?

Hi Volko,

Thanks for sharing your idea! For the time being, I am working on the
calculation of Euclidean distance between two endpoints of a curved line.
This line is selected in ROIs Manager. Could you please explain more about
how to measure the distance between the endpoints?

Best wishes,

Yuhong



--
Sent from: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.1557.x6.nabble.com%2F&amp;data=02%7C01%7Cvs64%40leicester.ac.uk%7C08e665dc746d45e1e8d108d70a2df6ae%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C636989064860380068&amp;sdata=reHz8Q5jf6IAccMulrMPhV4dBVOTUcVrAsYvpq0P%2FPk%3D&amp;reserved=0

--
ImageJ mailing list: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&amp;data=02%7C01%7Cvs64%40leicester.ac.uk%7C08e665dc746d45e1e8d108d70a2df6ae%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C636989064860380068&amp;sdata=u%2BMLctvlDyQknWuGnu%2Bv4FIjEvxu9cCYoGtOc1xpfZg%3D&amp;reserved=0

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