1,457 reputation
222
bio website physikalischebiologie.de/…
location Frankfurt, Germany
age 28
visits member for 1 year, 8 months
seen 18 hours ago

Sep
30
comment Image segmentation and object separation in 3D using Mathematica
Nice approach, thanks! I will try your approach on the data and keep you informed.
Sep
30
awarded  Benefactor
Sep
30
comment Image segmentation and object separation in 3D using Mathematica
Wow, thanks very much for the improvements and time you investigated on this problem! I especially like the parallelization, since runtime is always an issue when having large datasets. I think that the approaches you might be very helpful also in other segmentation attempts. I totally agree with you: The object separation algorithm you propose seems to be the best one can do with the data in order to split the objects. Therefore, I accepted your detailed answer and awarded the bounty to you. Thanks again!
Sep
30
accepted Image segmentation and object separation in 3D using Mathematica
Sep
27
comment Image segmentation and object separation in 3D using Mathematica
@Hector: Yeah, good idea with the beer and postcard ;) Maybe a postcard with a beer on it?
Sep
27
comment Image segmentation and object separation in 3D using Mathematica
Yes. The approach in the answer gives interesting results but doesn't give a satisfying segmentation of the objects. The objects are heavily oversegmented and seem to get spherical by the segmentation method. I think the ideas mentioned are very good but they need further optimization to achieve better segmentation. Especially the binarization and preprocessing need to be improved.
Sep
27
revised Image segmentation and object separation in 3D using Mathematica
added approach by UDB
Sep
26
comment Image segmentation and object separation in 3D using Mathematica
There is a comma missing in the function distcompiled after disttab.
Sep
26
awarded  Good Question
Sep
26
accepted How to scale edge length and keep layout of edge-weighted Graph?
Sep
26
comment How to scale edge length and keep layout of edge-weighted Graph?
Thanks for that information and the edit. This looks just like what I was looking for ;)
Sep
26
comment How to scale edge length and keep layout of edge-weighted Graph?
Interesting approach, thanks very much! The problem I see is that the edges are indeed scaled by some factor, but it doesn't directly represent the edge weights that are written on the edges. Look at the lower part (vertices 65,67,61,63 to 66,68,62,64) for example. There you have edges with weights 17 and 7, respectively. But, the edge length looks about the same whereas the difference is 10. The left edges should therefore be at least twice as long.
Sep
25
comment Image segmentation and object separation in 3D using Mathematica
The non-convexity of certain objects could indeed be a problem which might be fixed by merging some of the objects back together after they have been split by your proposed method. I will try the processing chain on my data and keep you informed.
Sep
25
comment Image segmentation and object separation in 3D using Mathematica
Perfect answer! Thanks very much! I can't wait to try it on my data ;)
Sep
25
comment Slice through Graphics3D
Yes, you are right. I forgot to add the last bit of code I created :)
Sep
25
revised Slice through Graphics3D
added 402 characters in body
Sep
25
answered Slice through Graphics3D
Sep
19
accepted Labelling of multiple BarChart elements with “Stacked” layout
Sep
19
asked Labelling of multiple BarChart elements with “Stacked” layout
Sep
16
comment Image segmentation and object separation in 3D using Mathematica
@belisarius: No. There is currently no possibility to increase the sample density in z. It is due to the optical properties of the microscope the images are aquired with. I am thinking about using something like Watershed segmentation in 3D to cope with the problem. But since there is no 3D implementation in MMA I will have to implement it or use another software.