[Tubetk-developers] TubeTK

[Stephen Aylward]

Hi,

If your data is in 3D, we might be able to help.

The contrast seems to be generally good, but the crossing small roots
might be difficult to separate - the 3D resolution will probably be
more of a factor than the contrast.

If you have a 3D volume, we could give it a try.

Stephen

On Tue, Jun 24, 2014 at 11:13 PM, eli rosen <elirosen at gmail.com> wrote:
> Thanks for your message, Stephen. It certainly looks like Tubetk could be
> interesting. I may attempt to start playing with it for my application,
> segmenting root networks of plants, via the 3D Slicer implementation. I've
> attached an image showing a representation of my data, and initial attempts
> at segmentation using Ilastik. For roots in soil, Ilastik was not able to
> discriminate between high contrast areas based on shape (I care about the
> roots but not the soil).
>
> Anyway, thanks again and I look forward to playing with this!
>
> Best,
> Eli
>
>
> On Mon, Jun 23, 2014 at 1:39 PM, Stephen Aylward
> <stephen.aylward at kitware.com> wrote:
>>
>> The methods are generally (mathematically) insensitive to intensity
>> variations.
>>
>> See the attached images for vessel enhancement --  Left: input.
>> Right: output.
>>
>> The extraction of centerlines is equally insensitive.
>>
>> s
>>
>> On Mon, Jun 23, 2014 at 1:35 PM, Ricardo Ortiz
>> <ricardo.ortiz at kitware.com> wrote:
>> > Hi Eli,
>> >
>> > It great that you are looking into TubeTK!
>> > I think the TubeTK folks should be able to answer that question with
>> > more
>> > expertise than I would.
>> > I am forwarding your email to the developers list.
>> >
>> > Cheers,
>> >
>> > /Ricardo
>> >
>> >
>> > On Mon, Jun 23, 2014 at 11:47 AM, eli rosen <elirosen at gmail.com> wrote:
>> >>
>> >> Hi Ricardo,
>> >>
>> >> I'm taking a peek at TubeTK now, and it looks really neat. Have you
>> >> evaluated its performance on any low contrast datasets? It looks like
>> >> you
>> >> have some really nice contrast from the MRI and REUS data. Just curious
>> >> how
>> >> well the segmentation works with lower contrast, which I have from my
>> >> process.
>> >>
>> >> Thanks!
>> >>
>> >> -Eli
>> >>
>> >>
>> >> On Sat, Jun 21, 2014 at 11:35 AM, Ricardo Ortiz
>> >> <ricardo.ortiz at kitware.com> wrote:
>> >>>
>> >>> http://tubetk.org/
>> >>>
>> >>> /Ricardo
>> >>>
>> >>> Sent from phone, please excuse terseness and typos.
>> >>
>> >>
>> >
>> >
>> > _______________________________________________
>> > Tubetk-developers mailing list
>> > Tubetk-developers at public.kitware.com
>> > http://public.kitware.com/mailman/listinfo/tubetk-developers
>> >
>>
>>
>>
>> --
>> ====================================================
>> Stephen R. Aylward, Ph.D.
>> Senior Director of Operations, North Carolina, Kitware, Inc.
>> http://www.kitware.com and http://www.aylward.org
>> (919) 969-6990 x300
>> ====================================================
>
>



-- 
====================================================
Stephen R. Aylward, Ph.D.
Senior Director of Operations, North Carolina, Kitware, Inc.
http://www.kitware.com and http://www.aylward.org
(919) 969-6990 x300
====================================================