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[Seg3D] Re: Export mask problem, documentation and wish list


Chronological Thread 
  • From: Sidnei Paciornik <sidnei@puc-rio.br>
  • To: seg3d@sci.utah.edu
  • Subject: [Seg3D] Re: Export mask problem, documentation and wish list
  • Date: Thu, 5 Jul 2012 14:49:12 -0300
Dear colleagues,

Did anyone process the message further below?

I got no response this far ...

I take this opportunity to report an apparent bug in the image import procedure. I had an image stack composed of RGB Tiff images. They were actually µCT images without color, but recorded with 3 channels with equal values.

When opening this stack in Seg3D some characteristic of the files makes the program interpret very different scales for the z and (x,y) directions. As a result, the image appears terribly stretched in the z direction.

If I first convert the RGB 24 bit images to single channel 8 bit everything works fine. For that matter, I was able to load and process a 2000x2000x2200 stack in a Linux system running on an i7-980 with 24 Gb RAM. The program is perfectly stable.

Thank you very much.

Prof. Sidnei Paciornik
Grupo de Análise de Imagens e Microscopia Digital
DEMa - Departamento de Engenharia de Materiais
PUC-Rio
Rua Marquês de São Vicente 225
Prédio Leme, Sala 501L
Gávea - Rio de Janeiro - RJ
22451-900 - Brasil
tel: (55)(21)3527-1243


On Wed, Jun 27, 2012 at 11:30 PM, Sidnei Paciornik <sidnei@puc-rio.br> wrote:
Hi there,

I have mentioned this to Ayla, but I am not sure if there was a chance to check it.

When I export a mask as bmp's or tiff's, the images are scaled between zero and one and the segmented regions are invisible. 

Of course I can rescale the intensities in almost any IP program, but I think the images should be automatically scaled to 0-255 or, at least, allow this option.

One more point: where can I find an UP TO DATE doc about Seg3D2 functions? Many are pretty self evident, but some are not. Is there a wiki or complete help? I did find some tutorials, but they were incomplete and seemed outdated.

Having said that, I think Seg3D2 is just outstanding. It is powerful, fast and very easy to use. The interface is one of the best I have seen. I hope you can continue its development.

If you allow me a wish list:
- measurement of objects sizes and shapes with a data file output (I am aware of the connected component size function but I cannot figure how to extract the size measurements - all I could do was  segment the component size image based on size/greyscale).
- transparency control of isosurfaces in 3D view.

Regards,

Prof. Sidnei Paciornik
Grupo de Análise de Imagens e Microscopia Digital - Image Analysis and Digital Microscopy Group
DEMa - Departamento de Engenharia de Materiais - Materials Engineering Department
PUC-Rio - Catholic University of Rio de Janeiro
Rua Marquês de São Vicente 225
Prédio Leme, Sala 501L
Gávea - Rio de Janeiro - RJ
22451-900 - Brasil
tel: (55)(21)3527-1243 
Dear colleagues,

Did anyone process the message below?

I got no response this far ...

I take this opportunity to report an apparent bug in the image import procedure. I had an image stack composed of RGB Tiff images. They were actually µCT images without color, but recorded with 3 channels with equal values.

When opening this stack in Seg3D some characteristic of the files makes the program 

On Wed, Jun 27, 2012 at 11:30 PM, Sidnei Paciornik <sidnei@puc-rio.br> wrote:
Hi there,

I have mentioned this to Ayla, but I am not sure if there was a chance to check it.

When I export a mask as bmp's or tiff's, the images are scaled between zero and one and the segmented regions are invisible. 

Of course I can rescale the intensities in almost any IP program, but I think the images should be automatically scaled to 0-255 or, at least, allow this option.

One more point: where can I find an UP TO DATE doc about Seg3D2 functions? Many are pretty self evident, but some are not. Is there a wiki or complete help? I did find some tutorials, but they were incomplete and seemed outdated.

Having said that, I think Seg3D2 is just outstanding. It is powerful, fast and very easy to use. The interface is one of the best I have seen. I hope you can continue its development.

If you allow me a wish list:
- measurement of objects sizes and shapes with a data file output (I am aware of the connected component size function but I cannot figure how to extract the size measurements - all I could do was  segment the component size image based on size/greyscale).
- transparency control of isosurfaces in 3D view.

Regards,

Prof. Sidnei Paciornik
Grupo de Análise de Imagens e Microscopia Digital - Image Analysis and Digital Microscopy Group
DEMa - Departamento de Engenharia de Materiais - Materials Engineering Department
PUC-Rio - Catholic University of Rio de Janeiro
Rua Marquês de São Vicente 225
Prédio Leme, Sala 501L
Gávea - Rio de Janeiro - RJ
22451-900 - Brasil
tel: (55)(21)3527-1243 


  • [Seg3D] Re: Export mask problem, documentation and wish list, Sidnei Paciornik, 07/05/2012

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