Posted by
Jason Miller on
Jan 14, 2016; 2:54pm
URL: http://imagej.273.s1.nabble.com/Mitochondrial-analysis-on-z-stack-tp5015379p5015382.html
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:startFor simpler 3d segmentation, you can also use the built-in 3D objects
counter function:
http://fiji.sc/3D_Objects_CounterThere 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:startIt'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:
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"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>
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