http://imagej.273.s1.nabble.com/Fwd-fiji-devel-Re-tracking-algorithms-tp3687323.html
I used the program from A. Serge and N. Berteaux to track quantum
Nat Methods. 2008 Aug;5(8):687-94
from G. Danuser's group that was rather complicated for my
Nat Methods. 2008 Aug;5(8):695-702.
There is also a nice review from E. Meijering that you can download here:
emitters). This could be useful for the first steps of tracking.
>
> Hi Wilhelm,
> I hadn't looked at that. Thanks for the tip!
> Nick
>
> On Mon, Aug 9, 2010 at 8:28 AM, Wilhelm Burger <
[hidden email]> wrote:
>>
>> Hi Nicolas,
>>
>> did you look at the Image_Stabilizer plugin listed on
>>
http://rsbweb.nih.gov/ij/plugins/index.html (
http://www.kangli.org/>> code/Image_Stabilizer.html)? It is apparently based on the Lucas-
>> Kanade tracker, which is a commonly used standard algorithm (at least
>> for 2D tracking).
>>
>> --Wilhelm
>>
>>
>> On 8 Aug., 21:38, Nick Perry <
[hidden email]> wrote:
>> > Hi all,
>> >
>> > *My goal:*
>> > I'm about to write a tracking class, which tracks points over multiple time
>> > frames in 3D (or 2D). I looked on the Fiji website and it looks like there
>> > really only exists a 2D tracker, a manual tracker, and ToAST (which also
>> > seems to be 2D over time, if the plugin hasn't been significantly modified
>> > from the paper describing it).
>> >
>> > Does anyone have any suggestions for potential, robust-as-possible
>> > algorithms? Ideally it should be able to handle a few particles, to many
>> > hundreds, and be generally applicable in terms of application areas. I am
>> > mostly interested in either: (a) something that has already been written by
>> > Fiji developers (like the extrema finding class I hadn't known about); or
>> > (b) if there is some prevailing algorithm out there that I haven't read
>> > about that would make this more useful to others. Ideally, I'd like to make
>> > an algorithm that other people *want* use, otherwise I find it to be a waste
>> > of time. So it should be able to do the things people here generally would
>> > want out of a tracker (as much as possible).
>> >
>> > *My own thoughts, approaches:*
>> > I've done some research of my own, and specifically focused on the following
>> > algorithms:
>> >
>> > - "StarryNite," Bao et al. 2006 "Automated cell lineage tracing in
>> > Caenorhabditis elegans" (
>> > - Sbalzarini and Koumoutsakos, 2005 "Feature point tracking and trajectory
>> > analysis for video imaging in cell biology"
>> > - A review by Y. Kalaidzidis, 2007 "Intracellular objects tracking"
>> > - IPAN, Verestoy and Chetverikov, 1998 "Tracking feature points: A new
>> > algorithm"
>> >
>> > I think if I make an algorithm, it would be more of a combination of
>> > StarryNite, and the algorithm described by Sbalzarini and Koumousakos.
>> >
>> > Specifically, I would use a greedy approach to try to pick the best track
>> > "connections," and my greedy criterion would actually be a combination of
>> > many aspects of the objects being tracked, including:
>> >
>> > - the position of the object in frame t+1 is "similar enough" to frame t.
>> > - how similar the potential object in frame t+1 looks compared to the object
>> > in frame t (intensity, size, shape)
>> >
>> > The plugin should also allow for entry/exit of objects, as well as allow
>> > developers to create additional classes that incorporate application
>> > specific information into the track assignments. For example, in the case of
>> > C. elegans development, I would try to create a system which allows for a
>> > user to incorporate information on the shape of the objects (round,
>> > condense, or elongated, which should match certain timing criterion in order
>> > to be valid) to more intelligently assign tracks.
>> >
>> > Again, these are some of my ideas, and if any of you have any input on other
>> > algorithms I should take a look at, or other aspects of tracking you think I
>> > should include in my algorithm, please let me know! It would be much
>> > appreciated!
>> >
>> > Cheers,
>> > Nick
>> >
>> > --
>> >
[hidden email]
>> > 425.308.2550
>> > @nick_perry
>>
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>
>
>
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> @nick_perry
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