active contours being slow and crashes segmenting 3D image stacks

[Jingjing]

Dear Icy team,

I was trying to segment some 3D stacks by edge (cell boundaries) and found that while active contours worked beautifully on my 2D images before, it runs quite slowly on 3D and sometimes crashes or shows an "out of memory" message.

I find it quite odd because I'm using an intel 8 core CPU 2.4GHz, 32G RAM, 64 bit, (win 8.1 system) and I gave Icy full use of the memory. I uploaded the small stack I used for testing and the 3D seeds generated from thresholding here, and it would be much appreciated if you could help me check what went wrong in my case. 

Thanks very much,

Jingjing

[Alexandre Dufour]

Dear Jingjing,

I think the issue you are experiencing results from the spatial resolution of your dataset.

After loading your sample inside Icy, I noticed that the metadata (more specifically the pixel size) seems incorrect (10mm in the planar direction seems a bit odd!), however the axial (Z) resolution seems reasonable (1 micron).

The active contours plugin relies on these values to calculate the sampling of the deformable mesh, and the parameter (in the 3D case) is expected in “microns” (instead of pixels in 2D). As a result, the out of memory error is a direct consequence of creating massively super-sampled mesh w.r.t. the data resolution.

I would suggest inserting the correct metadata (using the “Edit” button in the Inpector’s "Sequence properties” panel), and then adjust a reasonable contour sampling in microns (I usually choose 3 or 4 times the planar resolutions to begin with, and reduce if necessary).

Let me know if this works

Cheers

Alexandre

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<filtered 3D test.tif><filtered 3D test seeds roi.xml>

[Jingjing]

Dear Alexandre,

Yes it works!! Many thanks for your quick reply - now it runs very fast and gives beautifully promising results, and I'll play with the active contours parameters to make the contours closer to the edges (now the identified objects are smaller than the cells).

Thanks again,

Jingjing