Blood vessel branching analysis

[Schaffer, Beverly]

Hello Everyone,

 

I'm a complete novice with ImageJ software. I want to use the software
to analyze both the size and number of branches in quail embryo blood
vessels. I've seen papers that reference ImageJ as the software used for
this analysis, but I haven't been able to find anything more specific.
I've tried searching the help function of ImageJ without success.

 

Does anyone know or have an idea how this can be done?

 

Beverly Schaffer, PhD

Senior Research Associate

University of Texas Health Science Center San Antonio

Greehey Children's Cancer Research Institute

[hidden email]

[Elizabeth Crowell]

Hello,

I know how I might measure these things by hand, but I'm especially interested
in knowing if anyone has found a way to automate this type of measurement!
My colleagues have a fundamentally similar problem in measuring root length and
architecture, or leaf veins.  Would it be possible to automatically identify
the nodes or branchpoints and measure the length of the fibers?

In any case, by hand, you may use the segmented line tool available in the menu
bar.  Right click the line tool to obtain the segmented line tool option.
Using that tool you can trace a line along the blood vessels in your image, and
measure their length for example, using Analyze/Measure (or simply hit Ctrl+M).
You wrote that you would like to measure the "size" of the blood vessels, but
size could mean any number of things.  Are you interested in measuring length,
diameter, surface area???

You wrote that you would like to measure the "size" of the blood vessels, but
size could mean any number of things.  Are you interested in measuring length,
diameter, surface area???

Elizabeth Crowell


Laboratoire de Biologie Cellulaire
INRA / Institut Jean-Pierre Bourgin
Route de Saint-Cyr
78026 Versailles cedex
FRANCE

Tel: [phone]
Fax: [phone]




Selon "Schaffer, Beverly" <[hidden email]>:

> Hello Everyone,
>
>
>
> I'm a complete novice with ImageJ software. I want to use the software
> to analyze both the size and number of branches in quail embryo blood
> vessels. I've seen papers that reference ImageJ as the software used for
> this analysis, but I haven't been able to find anything more specific.
> I've tried searching the help function of ImageJ without success.
>
>
>
> Does anyone know or have an idea how this can be done?
>
>
>
> Beverly Schaffer, PhD
>
> Senior Research Associate
>
> University of Texas Health Science Center San Antonio
>
> Greehey Children's Cancer Research Institute
>
> [hidden email]
>

[Jason Miller-2]

Since 2005, we've been developing such a tool, our Vascular Netwook  
Toolkit, thru Truman's undergraduate interdisciplinary Mathematical  
Biology program.  Contact me directly by email and I can tell you more.

Jason

==========================
Jason Miller, Ph.D.
[hidden email]
660.785.7430 (work)
660.956.0259 (universal)
http://mathbio.truman.edu
~~~  sent from iPhone ~~~

On Jul 16, 2009, at 9:05, Elizabeth Crowell  
<[hidden email]> wrote:

> Hello,
>
> I know how I might measure these things by hand, but I'm especially  
> interested
> in knowing if anyone has found a way to automate this type of  
> measurement!
> My colleagues have a fundamentally similar problem in measuring root  
> length and
> architecture, or leaf veins.  Would it be possible to automatically  
> identify
> the nodes or branchpoints and measure the length of the fibers?
>
> In any case, by hand, you may use the segmented line tool available  
> in the menu
> bar.  Right click the line tool to obtain the segmented line tool  
> option.
> Using that tool you can trace a line along the blood vessels in your  
> image, and
> measure their length for example, using Analyze/Measure (or simply  
> hit Ctrl+M).
> You wrote that you would like to measure the "size" of the blood  
> vessels, but
> size could mean any number of things.  Are you interested in  
> measuring length,
> diameter, surface area???
>
> You wrote that you would like to measure the "size" of the blood  
> vessels, but
> size could mean any number of things.  Are you interested in  
> measuring length,
> diameter, surface area???
>
> Elizabeth Crowell
>
>
> Laboratoire de Biologie Cellulaire
> INRA / Institut Jean-Pierre Bourgin
> Route de Saint-Cyr
> 78026 Versailles cedex
> FRANCE
>
> Tel: [phone]
> Fax: [phone]
>
>
>
>
> Selon "Schaffer, Beverly" <[hidden email]>:
>
>> Hello Everyone,
>>
>>
>>
>> I'm a complete novice with ImageJ software. I want to use the  
>> software
>> to analyze both the size and number of branches in quail embryo blood
>> vessels. I've seen papers that reference ImageJ as the software  
>> used for
>> this analysis, but I haven't been able to find anything more  
>> specific.
>> I've tried searching the help function of ImageJ without success.
>>
>>
>>
>> Does anyone know or have an idea how this can be done?
>>
>>
>>
>> Beverly Schaffer, PhD
>>
>> Senior Research Associate
>>
>> University of Texas Health Science Center San Antonio
>>
>> Greehey Children's Cancer Research Institute
>>
>> [hidden email]
>>

[Michael Doube]

Beverly

You could try AnalyzeSkeleton_ after skeletonising your network, which
gives branch lengths, junction counts etc.:

http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:analyzeskeleton:start
http://imagejdocu.tudor.lu/doku.php?id=plugin:morphology:skeletonize3d:start

If you want thicknesses, you could try the Local Thickness plugin, and
correlate the 2 resulting images:

http://www.optinav.com/Local_Thickness.htm

Mike

Schaffer, Beverly wrote:

> Hello Everyone,
>
>  
>
> I'm a complete novice with ImageJ software. I want to use the software
> to analyze both the size and number of branches in quail embryo blood
> vessels. I've seen papers that reference ImageJ as the software used for
> this analysis, but I haven't been able to find anything more specific.
> I've tried searching the help function of ImageJ without success.
>
>  
>
> Does anyone know or have an idea how this can be done?
>
>  
>
> Beverly Schaffer, PhD
>
> Senior Research Associate
>
> University of Texas Health Science Center San Antonio
>
> Greehey Children's Cancer Research Institute
>
> [hidden email]

[Elizabeth Crowell]

Hello,
Thank you to all those who replied to my question about analyzing
fibers/networks in images!  Although I have never needed to do such
measurements myself, I will certainly forward your responses and contact
information to my colleagues who are doing this work.

Sincerely,
Elizabeth Crowell

Laboratoire de Biologie Cellulaire
INRA / Institut Jean-Pierre Bourgin
Route de Saint-Cyr
78026 Versailles cedex
FRANCE

Tel: [phone]
Fax: [phone]