From ricardo.ortiz at kitware.com Mon Jun 23 13:35:41 2014 From: ricardo.ortiz at kitware.com (Ricardo Ortiz) Date: Mon, 23 Jun 2014 13:35:41 -0400 Subject: [Tubetk-developers] TubeTK In-Reply-To: References: Message-ID: 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 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 > wrote: > >> http://tubetk.org/ >> >> /Ricardo >> >> Sent from phone, please excuse terseness and typos. >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.aylward at kitware.com Mon Jun 23 13:39:12 2014 From: stephen.aylward at kitware.com (Stephen Aylward) Date: Mon, 23 Jun 2014 13:39:12 -0400 Subject: [Tubetk-developers] TubeTK In-Reply-To: References:

Message-ID: 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 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 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 >> 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 ==================================================== -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2014-06-16 at 8.57.48 AM.png Type: image/png Size: 47440 bytes Desc: not available URL: From stephen.aylward at kitware.com Fri Jun 27 10:17:39 2014 From: stephen.aylward at kitware.com (Stephen Aylward) Date: Fri, 27 Jun 2014 10:17:39 -0400 Subject: [Tubetk-developers] TubeTK In-Reply-To: References:

Message-ID: 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 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 > 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 >> 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 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 >> >> 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 ==================================================== From ricardo.ortiz at kitware.com Mon Jun 23 13:35:41 2014 From: ricardo.ortiz at kitware.com (Ricardo Ortiz) Date: Mon, 23 Jun 2014 13:35:41 -0400 Subject: [Tubetk-developers] TubeTK In-Reply-To: References: Message-ID: 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 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 > wrote: > >> http://tubetk.org/ >> >> /Ricardo >> >> Sent from phone, please excuse terseness and typos. >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.aylward at kitware.com Mon Jun 23 13:39:12 2014 From: stephen.aylward at kitware.com (Stephen Aylward) Date: Mon, 23 Jun 2014 13:39:12 -0400 Subject: [Tubetk-developers] TubeTK In-Reply-To: References: