Tracking particles in time series of z-stacks

[Gary G. Li-2]

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Greetings:
I am looking for software tools for tracking fluorescent particles in time
series of z-stacks.  Instead of the trajectories, I am more interested in
fluctuation of the fluorescent intensities of the particles over time.
Please share with me your experience and insight.
Regards
Gary G. Li, Ph.D.
Microscopy Core Facility Manager
NIH/NIDA, Baltimore, MD 21224

[Sanghoon Oh]

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Dear Gary,

Imaris can track particles in 3D. Also it can reconnect missing particles in certain time points, e.g. when the particle's brightness went down and did not acquired properly.
Thanks.

Sincerely,
Sanghoon

---------------------------------------------------
Sanghoon Oh, Ph.D. ([hidden email])

Memorial Sloan-Kettering Cancer Center
Molecular Cytology Core Facility
Tel.[phone]
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-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Gary G. Li
Sent: Wednesday, March 21, 2012 1:05 PM
To: [hidden email]
Subject: Tracking particles in time series of z-stacks

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Greetings:
I am looking for software tools for tracking fluorescent particles in time
series of z-stacks.  Instead of the trajectories, I am more interested in
fluctuation of the fluorescent intensities of the particles over time.
Please share with me your experience and insight.
Regards
Gary G. Li, Ph.D.
Microscopy Core Facility Manager
NIH/NIDA, Baltimore, MD 21224


 
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[John Oreopoulos]

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Hi Gary,

There are a number of particle tracking plugins at the ImageJ plugins page:

http://rsbweb.nih.gov/ij/plugins/index.html

Here are a few:

http://rsbweb.nih.gov/ij/plugins/tracker.html
http://rsbweb.nih.gov/ij/plugins/multitracker.html
http://bigwww.epfl.ch/sage/soft/spottracker/
http://www.imagescience.org/meijering/software/mtrackj/

I think if you use the following plugin with the basic tracker plugin, it will do what you want it to do (intensity measurements), but the other plugins listed above might also have the same feature built in already:

http://rsbweb.nih.gov/ij/plugins/measure-track/index.html

I haven't had much experience with these sorts of plugins, but given that there are so many, it seems to be a common type of measurement for others. Consider looking at the Fiji repository as well.

John Oreopoulos


On 2012-03-21, at 1:05 PM, Gary G. Li wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Greetings:
> I am looking for software tools for tracking fluorescent particles in time
> series of z-stacks.  Instead of the trajectories, I am more interested in
> fluctuation of the fluorescent intensities of the particles over time.
> Please share with me your experience and insight.
> Regards
> Gary G. Li, Ph.D.
> Microscopy Core Facility Manager
> NIH/NIDA, Baltimore, MD 21224