http://imagej.273.s1.nabble.com/Fwd-fiji-devel-Re-tracking-algorithms-tp3687323p3687324.html
> ---------- Forwarded message ----------
> From: Christophe Leterrier <
[hidden email]>
> Date: 2010/8/9
> Subject: Re: [fiji-devel] Re: tracking algorithms?
> To: Nick Perry <
[hidden email]>
>
>
> I'm not an image processing specialist, but I'm following the
> applications of particle tracking in biology.
>
> I used the program from A. Serge and N. Berteaux to track quantum
> dots-labeled surface particles, and it worked quite well:
>
> Sergé A, Bertaux N, Rigneault H, Marguet D.
> Dynamic multiple-target tracing to probe spatiotemporal cartography of
> cell membranes.
> Nat Methods. 2008 Aug;5(8):687-94
> Single-particle tracking (SPT) of quantum-dots has been a proeminent
> application of tracking algorithms for several years now, with the
> added complexity that these molecules are blinking, so an individual
> QD can disappear from several frames before reappearing in the
> subsequent ones.
>
> In the same issue of Nature Methods, I remember reading another paper
> from G. Danuser's group that was rather complicated for my
> mathematically-challenged skills, but claiming to solve the 2D+t
> trajectories assignment problem as a whole:
>
> Jaqaman K, Loerke D, Mettlen M, Kuwata H, Grinstein S, Schmid SL, Danuser G.
> Robust single-particle tracking in live-cell time-lapse sequences.
> Nat Methods. 2008 Aug;5(8):695-702.
>
> There is also a nice review from E. Meijering that you can download here:
>
http://www.imagescience.org/meijering/publications/?p=1001>
> Finally, several recent short communications in Nature Methods have
> adressed the problem of the most efficient and fast ways of detecting
> and localizing spots on images (in order to speed up superresolutive
> imaging modalities based on localization of single fluorescent
> emitters). This could be useful for the first steps of tracking.
>
>
> Christophe Leterrier
>
>
> 2010/8/9 Nick Perry <
[hidden email]>
>>
>> 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
>>>
>>> --
>>> You received this message because you are subscribed to the Google Groups "Fiji-devel" group.
>>> To post to this group, send email to
[hidden email].
>>> To unsubscribe from this group, send email to
[hidden email].
>>> For more options, visit this group at
http://groups.google.com/group/fiji-devel?hl=en.
>>>
>>
>>
>>
>> --
>>
[hidden email]
>> 425.308.2550
>> @nick_perry
>>
>> --
>> You received this message because you are subscribed to the Google Groups "Fiji-devel" group.
>> To post to this group, send email to
[hidden email].
>> To unsubscribe from this group, send email to
[hidden email].
>> For more options, visit this group at
http://groups.google.com/group/fiji-devel?hl=en.
>