Example: Scikit-image and trackpy (bubble tracking in foams)

[Nelle Varoquaux]

On 20 November 2014 20:22, Emmanuelle Gouillart
<emmanuelle.gouillart at nsup.org> wrote:
>
> Very nice! I just tweeted about it :-).
>
> How good is that trackpy library? On Tuesday I was giving a presentation
> about scikit-image and someone in the audience asked me if I knew some
> good tools for 2D/3D + time image processing, for example for tracking
> particles/cells. I didn't know any, and actually I don't know whether
> there exist some "classical" and robust algorithms for particle tracking
> (like median filter for denoising, otsu thresholding, etc.), or if
> everything is very application-dependent. What is your experience about
> this?

There are cell tracking specific softwares such as cell cognition (C++
+ python). I think there are a lot of very specific software for cell
tracking depending on what the data is.
Cheers,
N

>
> Best,
> Emmanuelle
>
>
> On Thu, Nov 20, 2014 at 01:05:24PM -0500, François Boulogne wrote:
>> Hi,
>
>> Just for your information, I wrote an example based on my research to
>> show the use of scikit-image with trackpy for feature detection and
>> tracking.
>> http://nbviewer.ipython.org/github/soft-matter/trackpy-examples/blob/master/notebooks/custom_feature_detection.ipynb
>
>> Hopefully, this might be helpful for future workshops or presentations.
>
>> Best,
>
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