active contours slows down half-way in a run

[Jingjing]

Dear Alexandre and Stephane,

I encountered a small problem when running active contours - it's very fast in the beginning when the cell contours are evolving, but once the contours reach the cell boundaries and appear "fixed", it suddenly slows down and takes ages to finish (actually I didn't wait for it to finish because it takes too long, and pressed the stop button prematurely instead to get the results...) I attached a screenshot when it halts. 

Is it normal or is there anything I can do to speed it up?

Many thanks,

Jingjing

[Alexandre Dufour]

Dear Jingjing,

Two ways to accelerate the process:

— Increase the “Evolution time step” parameter (beware: causes instabilities if too high)

— Increase the “Convergence criterion” parameter (to increase the detection rate of non-motile contours)

— Last resort (not recommended): reduce the maximum number of iterations.

Let me know if this helps

Alexandre

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<active contours slows down in the middle of a run.png>

[Jingjing]

Dear Alexandre,

Thanks! Just tried all three - increasing the evolution time step gave larger objects, increasing the convergence criterion didn't show significant difference (I didn't bring it up to a crazy level though:)). and the least favourite "reducing iteration" worked! 

So I'll use the last resort while keeping the max iteration number as high as possible. 

Best,

Jingjing

[ArpnSharma]

Hello,

Sorry if I should be posting somewhere else, but I found this post to be most relevant to my question. 

Background:

I want to track cell (2d+t). The cells are not evenly stained and when thresholding I get multiple "particles/blobs" for each cell. 

I have found active contours does the best job in identifying individual cells. It is "slow" when going through an image sequence of >150. I can try the suggestions you gave the OP concerning the speed. 

Question:

Is there a way to automate cell detection by active contours and then track the cells? Ideally, I would like to automate everything so that I can let it in my computer while I can be doing experiments. 

Thanks

Arpn 

[Alexandre Dufour]

Hi Arpn,

You could the following protocol : http://icy.bioimageanalysis.org/protocol/Track_cell_intensity

Alexandre

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