Measuring distance between two points

[Liliana de Jesus Duarte Ferreira]

Dear all

Can anyone tell me how to measure the distance between two spots that are
in different sections of the same stack?

Thanks

Liliana







--
Liliana Ferreira
Plant Genetic Engineering Laboratory
Instituto de Tecnologia Química e Biológica
Av. Republica, Apartado 127
2781-901 Oeiras
Portugal

[hidden email]
phone: [phone]

[John Oreopoulos]

Hi Liliana,

First, I'm assuming you're talking about measuring the distance  
between two points in 3D space that have been captured in a single  
time point 3D stack and not a time-lapse 2D stack. A simple way to do  
this is to draw a line on one image of the stack that would intersect  
both spots of interest if they both occurred in the same image (You  
could add all images together to make this happen, draw the line, and  
then draw it again on the original stack). Then click Image->stacks-
 >reslice. This produces a new image that is a cross-section side on  
view of the stack along the line you drew, and you should now see  
both spots separated by some vertical and horizontal pixel distance.  
Now you need to know your lateral and axial pixel dimensions in order  
to calculate the distance. However, I'm not exactly sure how ImageJ  
draws reslice images from lines that were drawn on a diagonal. You  
might have to consider that when calculating the lateral distance.
I'm sure someone out there has already produced a much better ImageJ  
plugin would essentially do all of this for you by clicking on the  
two points of interest in the stack, but you may have to hunt around  
on the plugins part of the website to find that. Can anyone else  
recommend a plugin?

John Oreopoulos


On 20-Jun-08, at 11:07 AM, Liliana de Jesus Duarte Ferreira wrote:

> Dear all
>
> Can anyone tell me how to measure the distance between two spots  
> that are
> in different sections of the same stack?
>
> Thanks
>
> Liliana
>
>
>
>
>
>
>
> --
> Liliana Ferreira
> Plant Genetic Engineering Laboratory
> Instituto de Tecnologia Química e Biológica
> Av. Republica, Apartado 127
> 2781-901 Oeiras
> Portugal
>
> [hidden email]
> phone: [phone]

... [show rest of quote]

[Wayne Rasband]

> Can anyone tell me how to measure the distance between two spots that
> are
> in different sections of the same stack?

The 3D distance tool does this.

    http://rsb.info.nih.gov/ij/macros/tools/3D-Distance-Tool.txt

-wayne

[simon andrews (BI)]

 

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On
> Behalf Of Liliana de Jesus Duarte Ferreira
> Sent: 20 June 2008 16:08
> To: [hidden email]
> Subject: Measuring distance between two points
>
> Dear all
>
> Can anyone tell me how to measure the distance between two
> spots that are in different sections of the same stack?

It's just an extension of Pythagoras' theorem to do this in 3D.

ie

sqrt((x1-x2)**2 + (y1-y2)**2 + (z1-z2)**2)

You'll need to watch out that the distance between adjacent pixels in
the same stack probably won't be the same as the distance between the
same pixel in adjacent stacks so convert to real distances as early as
possible to keep things simple.

It may well be overkill for your case, but I wrote a plugin to this a
while back.  It requires fairly clean images and needs Java3D to be
installed, but it might be worth a look.

http://www.bioinformatics.bbsrc.ac.uk/projects/stackmeasure/

Simon.

[Dimiter Prodanov-2]

Hi,

take the Euclidean distance between points in 3D space:

D=sqrt ( (x1-x2)^2 + (y1-y2)^2 + (z1-z2)^2)

You have to calibrate x and y which will give you the focal plane
projection  and the the z-axis which will give you the depth.

best regards,

Dimiter

[Liliana de Jesus Duarte Ferreira]

Thanks John Oreopoulos, Wayne Rasband, Simon Andrews and Dimitir Prodanov
for the help.

Cheers,

Liliana

[radioradio]

Hi! Is it possible to reslice a cross-sectional stack along this 3d line?