Changing of position of domains over time

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

Changing of position of domains over time

anusuya pal
Hello,

I have a stack of domains which change the position over time and want to
follow the area of each domain with mean intensity over time. A typical
stack can be found here:

https://drive.google.com/open?id=0B-zIvUHKCb_zOUgtSnI2d1pnRHM

As you can see there are various types of domains, morphologically these
are very different from each other. I want to measure the mean intensity of
the similar domains over the time. And to do the selection of each domain,
I can use the freehand tool in ImageJ but the mean intensity depends on the
area of the sample.

Is there any method (in ImageJ or FIJI) so that the area of the domain
remains same and for each time, and can cover the domain properly?


Thanks
Anu

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

Re: Changing of position of domains over time

jerie
Dear Anu,

not sure what exactly we are looking at here, another strategy might be to
fluorescently label the compartment boundaries and use confocal imaging
which should give you data that are easier to analyse automatically.

My 2 cents, Jens

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Jens Rietdorf Visiting Scientist Fundação Oswaldo Cruz - Ministério da Saúde, Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Rio de Janeiro, Brasil.
Reply | Threaded
Open this post in threaded view
|

Re: Changing of position of domains over time

Michael Schmid-3
In reply to this post by anusuya pal
Hi Anu,

you may try the StackReg plugin with 'Affine' (affine transformation);
maybe run it twice.
Then the domains stay in place and you can select a domain once, then
run Image>Stacks>Plot z axis profile.


Michael
________________________________________________________________
On 11/09/2017 19:54, anusuya pal wrote:

> Hello,
>
> I have a stack of domains which change the position over time and want to
> follow the area of each domain with mean intensity over time. A typical
> stack can be found here:
>
> https://drive.google.com/open?id=0B-zIvUHKCb_zOUgtSnI2d1pnRHM
>
> As you can see there are various types of domains, morphologically these
> are very different from each other. I want to measure the mean intensity of
> the similar domains over the time. And to do the selection of each domain,
> I can use the freehand tool in ImageJ but the mean intensity depends on the
> area of the sample.
>
> Is there any method (in ImageJ or FIJI) so that the area of the domain
> remains same and for each time, and can cover the domain properly?
>
>
> Thanks
> Anu

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

Re: Changing of position of domains over time

anusuya pal
Thanks to everyone!

Anu

On 12-Sep-2017 5:44 AM, "Michael Schmid" <[hidden email]> wrote:

> Hi Anu,
>
> you may try the StackReg plugin with 'Affine' (affine transformation);
> maybe run it twice.
> Then the domains stay in place and you can select a domain once, then run
> Image>Stacks>Plot z axis profile.
>
>
> Michael
> ________________________________________________________________
> On 11/09/2017 19:54, anusuya pal wrote:
>
>> Hello,
>>
>> I have a stack of domains which change the position over time and want to
>> follow the area of each domain with mean intensity over time. A typical
>> stack can be found here:
>>
>> https://drive.google.com/open?id=0B-zIvUHKCb_zOUgtSnI2d1pnRHM
>>
>> As you can see there are various types of domains, morphologically these
>> are very different from each other. I want to measure the mean intensity
>> of
>> the similar domains over the time. And to do the selection of each domain,
>> I can use the freehand tool in ImageJ but the mean intensity depends on
>> the
>> area of the sample.
>>
>> Is there any method (in ImageJ or FIJI) so that the area of the domain
>> remains same and for each time, and can cover the domain properly?
>>
>>
>> Thanks
>> Anu
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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