Unable to implement VMTK VesselEnhancement filtering in Slicer 3.6

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Unable to implement VMTK VesselEnhancement filtering in Slicer 3.6

Sharmin Sultana
Hi
I am trying to compute the centerline of a tubular object.
I have installed slicer version 3.6.3 and then installed the VMTK extensions from the following repository.

http://ext.slicer.org/ext/Slicer-3-6/16157%2dlinux%2dx86_64/

But after extracting ROI from MRI data when I am trying to apply the VMTK vesselness filtering I could not find anything under the VesselEnhancement panel.

Please help me out why I am unable to find the parameters under VesselEnhancement. 

Thnaks.

--
Sharmin Sultana
Graduate Research Assistant
Department of Modeling, Simulation and Visualization Engineering
Frank Batten College of Engineering & Technology
Old Dominion University
Norfolk, VA-23529, USA


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Re: Unable to implement VMTK VesselEnhancement filtering in Slicer 3.6

Daniel Haehn
Hi Sharmin,

I think something went wrong. Could you check the error log?

Thx,
Daniel

On Mon, Jun 25, 2012 at 3:38 PM, Sharmin Sultana <[hidden email]> wrote:

> Hi
> I am trying to compute the centerline of a tubular object.
> I have installed slicer version 3.6.3 and then installed the VMTK extensions
> from the following repository.
>
> http://ext.slicer.org/ext/Slicer-3-6/16157%2dlinux%2dx86_64/
>
> But after extracting ROI from MRI data when I am trying to apply the VMTK
> vesselness filtering I could not find anything under the VesselEnhancement
> panel.
>
> Please help me out why I am unable to find the parameters under
> VesselEnhancement.
>
> Thnaks.
>
> --
> Sharmin Sultana
> Graduate Research Assistant
> Department of Modeling, Simulation and Visualization Engineering
> Frank Batten College of Engineering & Technology
> Old Dominion University
> Norfolk, VA-23529, USA
>
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Bioformat from LOCI

Murat Maga
Hi folks,

Would it be possible to support Bioformat library in Slicer? They have an impressive list of imaging formats that they can import. http://loci.wisc.edu/software/bio-formats

It would be great to be able to open some of those formats in Slicer right away.

M  

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Re: Bioformat from LOCI

madanrao
Hello Murat,

For Slicer to support, you need to convert images into .nrrd format (which is one of listed formats).

I hope this helps.

AM Mohan Rao

On Tue, Jun 26, 2012 at 11:03 AM, Murat Maga <[hidden email]> wrote:
Hi folks,

Would it be possible to support Bioformat library in Slicer? They have an impressive list of imaging formats that they can import. http://loci.wisc.edu/software/bio-formats

It would be great to be able to open some of those formats in Slicer right away.

M

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Re: Bioformat from LOCI

Julien Finet
While it's unlikely that we add new file format support, you can contribute an extension that supports new file format (reading or writing).
Let me know if you are interested with that project,  I can provide some pointers to you.
Julien.

On Tue, Jun 26, 2012 at 2:31 AM, Madan Rao <[hidden email]> wrote:
Hello Murat,

For Slicer to support, you need to convert images into .nrrd format (which is one of listed formats).

I hope this helps.

AM Mohan Rao


On Tue, Jun 26, 2012 at 11:03 AM, Murat Maga <[hidden email]> wrote:
Hi folks,

Would it be possible to support Bioformat library in Slicer? They have an impressive list of imaging formats that they can import. http://loci.wisc.edu/software/bio-formats

It would be great to be able to open some of those formats in Slicer right away.

M

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Re: Bioformat from LOCI

inorton
I looked at this a while back, but found openslide is mostly sufficient for my microscopy images

There has already been a good amount of work towards supporting bioformats as an ITK plugin:

http://www.vtk.org/Wiki/ITK_Release_4/Microscopy/File_Formats/Bio-Formats
http://www.itk.org/Wiki/ITK/Tcons/Agendas/2011_02_11#ITK_Readers_for_Microscopy_formats
http://public.kitware.com/pipermail/insight-users/2010-March/035566.html
http://lists.openmicroscopy.org.uk/pipermail/ome-users/2012-May/003041.html

However, BioFormats is GPL licensed, so it could not be part of the standard Slicer distribution. Maybe a build option.

It might also be possible to make it a Slicer extension which is built separately but loadable -- this is how the GPL'd CMTK is available -- but I don't know if extensions can introduce new ITK plugins... And the java dependencies might be tricky.

A bigger issue is internal slicer structures to support these kinds of images. Color images are supported, but multi-channel images are not really supported in a way that is useful for microscopy yet, as far as I know.



On Tue, Jun 26, 2012 at 9:02 AM, Julien Finet <[hidden email]> wrote:
While it's unlikely that we add new file format support, you can contribute an extension that supports new file format (reading or writing).
Let me know if you are interested with that project,  I can provide some pointers to you.
Julien.

On Tue, Jun 26, 2012 at 2:31 AM, Madan Rao <[hidden email]> wrote:
Hello Murat,

For Slicer to support, you need to convert images into .nrrd format (which is one of listed formats).

I hope this helps.

AM Mohan Rao


On Tue, Jun 26, 2012 at 11:03 AM, Murat Maga <[hidden email]> wrote:
Hi folks,

Would it be possible to support Bioformat library in Slicer? They have an impressive list of imaging formats that they can import. http://loci.wisc.edu/software/bio-formats

It would be great to be able to open some of those formats in Slicer right away.

M

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