http://imagej.273.s1.nabble.com/Fwd-fiji-devel-Re-tracking-algorithms-tp3687323p3687325.html
Thanks, I had not seen it, but like the mtrack2 plugin for following drosophila larvae
> Sorry for this, I mistakingly forwarded a fiji-devel post to the
> ImageJ mailing list.
>
> Christophe
>
> 2010/8/9 Christophe Leterrier <
[hidden email]>:
>> ---------- 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
>>>>
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>>>
>>>
>>>
>>> --
>>>
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>>> 425.308.2550
>>> @nick_perry
>>>
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