Mitochondrial analysis on z-stack

[Василий Попков]

Good time of a day, friends.

I have a z-stack of tmre colored mitochondria in a cell (red channel). I've
found an article, which is dealing with mitochondria morphology via
algorithms, but I can't really apply it - Im not good enough programmer
(well, I'm not at all).

So. It is quite easy to detect mitochondria on each slice with some kind of
"analyze particles" or similar things. BUT. There are same mitochondria on
different slices. Are there any plugins which can understand that "this and
this are the same mitochondria as on previous slice, this is new one"? And
somehow to analyze it. Volume will be ideal, but at least something.

Thank you a lot for you time. Any suggestions of what available plugins I
can use will be very helpful.

Vasily

Link to z-stack and article
https://www.dropbox.com/sh/af5hopz04ca8d73/AABIvB2SPf17I8h6rfNvbhS1a?dl=0

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[Jason Miller]

Hi Visaly-

I'm sure Thomas Bouldier will chime in here, but his 3D analysis suite
contains a range of options to do exactly what you are asking.

http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:start

For simpler 3d segmentation, you can also use the built-in 3D objects
counter function:

http://fiji.sc/3D_Objects_Counter

There are a huge range of other plugins out there that will count particles
in 3D (e.g. the Lipid Droplet Counter, but others as well):

http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:droplet_counter:start

It's a bit of trial and error to decide which of these is the simplest one
that works for you.

-Jason

-------

Jason Miller, MD, PhD

University of Michigan Kellogg Eye Center


Home address:

117 Worden Ave

Ann Arbor, MI 48103

Cell: [phone]

E-mail: *[hidden email] <[hidden email]>*


"Forgiveness does not change the past, but it does enlarge the future." -
Paul Boese

On Thu, Jan 14, 2016 at 7:22 AM, Василий Попков <[hidden email]>
wrote:

> Good time of a day, friends.
>
> I have a z-stack of tmre colored mitochondria in a cell (red channel). I've
> found an article, which is dealing with mitochondria morphology via
> algorithms, but I can't really apply it - Im not good enough programmer
> (well, I'm not at all).
>
> So. It is quite easy to detect mitochondria on each slice with some kind of
> "analyze particles" or similar things. BUT. There are same mitochondria on
> different slices. Are there any plugins which can understand that "this and
> this are the same mitochondria as on previous slice, this is new one"? And
> somehow to analyze it. Volume will be ideal, but at least something.
>
> Thank you a lot for you time. Any suggestions of what available plugins I
> can use will be very helpful.
>
> Vasily
>
> Link to z-stack and article
> https://www.dropbox.com/sh/af5hopz04ca8d73/AABIvB2SPf17I8h6rfNvbhS1a?dl=0
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Василий Попков]

Thank you a lot. Now I know where to look. I'm a little ashamed, because
now it seems obvious... But thanks :)

2016-01-14 17:59 GMT+03:00 Jason Miller <[hidden email]>:

> Hi Visaly-
>
> I'm sure Thomas Bouldier will chime in here, but his 3D analysis suite
> contains a range of options to do exactly what you are asking.
>
> http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:start
>
> For simpler 3d segmentation, you can also use the built-in 3D objects
> counter function:
>
> http://fiji.sc/3D_Objects_Counter
>
> There are a huge range of other plugins out there that will count particles
> in 3D (e.g. the Lipid Droplet Counter, but others as well):
>
>
> http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:droplet_counter:start
>
> It's a bit of trial and error to decide which of these is the simplest one
> that works for you.
>
> -Jason
>
> -------
>
> Jason Miller, MD, PhD
>
> University of Michigan Kellogg Eye Center
>
>
> Home address:
>
> 117 Worden Ave
>
> Ann Arbor, MI 48103
>
> Cell: [phone]
>
> E-mail: *[hidden email] <[hidden email]
> >*
>
>
> "Forgiveness does not change the past, but it does enlarge the future." -
> Paul Boese
>
> On Thu, Jan 14, 2016 at 7:22 AM, Василий Попков <[hidden email]>
> wrote:
>
> > Good time of a day, friends.
> >
> > I have a z-stack of tmre colored mitochondria in a cell (red channel).
> I've
> > found an article, which is dealing with mitochondria morphology via
> > algorithms, but I can't really apply it - Im not good enough programmer
> > (well, I'm not at all).
> >
> > So. It is quite easy to detect mitochondria on each slice with some kind
> of
> > "analyze particles" or similar things. BUT. There are same mitochondria
> on
> > different slices. Are there any plugins which can understand that "this
> and
> > this are the same mitochondria as on previous slice, this is new one"?
> And
> > somehow to analyze it. Volume will be ideal, but at least something.
> >
> > Thank you a lot for you time. Any suggestions of what available plugins I
> > can use will be very helpful.
> >
> > Vasily
> >
> > Link to z-stack and article
> >
> https://www.dropbox.com/sh/af5hopz04ca8d73/AABIvB2SPf17I8h6rfNvbhS1a?dl=0
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Vasily A Popkov
Lab.Structure and function of mitochondria
A.N.Belozersky Institute of Physico-Chemical Biology
Moscow State University

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