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


Chronological Thread 
  • From: "Ayla Khan" <ayla@sci.utah.edu>
  • To: seg3d@sci.utah.edu,Sidnei Paciornik <sidnei@puc-rio.br>
  • Subject: [Seg3D] Re: Re: Re: Export mask problem, TIFF load problem, documentation and wish list
  • Date: Thu, 11 Oct 2012 19:10:11 -0600
Hi Sidnei,

Seg3D 1.x had a scale tool, but it didn't make it into Seg3D 2. I'll look into what it would take to add it back into Seg3D 2.

Ayla

On Thu, 11 Oct 2012 09:06:15 -0300
 Sidnei Paciornik <sidnei@puc-rio.br> wrote:
Thank you Ayla,

One quick question: How do I define a scale for the images?

Regards,

Sidnei

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


On Thu, Oct 11, 2012 at 2:52 AM, Ayla Khan <ayla@sci.utah.edu> wrote:

Hi Sidnei,

We are currently working on a new manual to explain Seg3D's tools and
filters, which will be included in the next release. In the meanwhile, the
filter documentation for Seg3D 1.x more or less applies to Seg3D 2. We also
have a video presentation where the more important functionality is
demonstrated:
http://www.sci.utah.edu/gallery2/v/software/seg3d/video/user/.

Unfortunately, Seg3D only supports single channel greyscale files, so if
you have multi-channel and/or RGB data, it will have to be preprocessed
before importing into Seg3D. I've added your feature requests to our
tracking system and will see if they're feasible for the next release.

Thanks for the feedback,

Ayla

On Oct 8, 2012, at 4:52 PM, Sidnei Paciornik wrote:

Dear colleagues,

I am sending this message again. hoping that you can find time to deal
with it.

1) When I export a mask, the images are scaled between zero and one and
the segmented regions are not immediately visible when I open the file in
another program. 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.

2) I have noticed a weird behavior when opening TIFF files which are not
greyscale. If the pixels are RGB or indexed color Seg3D is able to open the
files but there is some scaling problem and the Z axis is terribly
stretched against the x-y scale. I have the same behavior in Seg3D2 for
Windows or Linux.

3) How do I set the x-y-z scale of an image in microns, etc.??

4) 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.

Thank you very much!

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



On Fri, Aug 17, 2012 at 9:51 PM, Sidnei Paciornik <sidnei@puc-rio.br>wrote:

Thanks Ayla, I was really worried about the lack of feedback ...

Keep in touch.

Regards,

Sidnei


On Fri, Aug 17, 2012 at 8:55 PM, Ayla Khan <ayla@sci.utah.edu> wrote:

Hi Sidnei,

Sorry about the delay in getting back to you - I'm looking into your
problem and wish list items, and will get back to you shortly.

Ayla

On Aug 10, 2012, at 6:26 AM, Sidnei Paciornik wrote:

Dear all,

Did the messages below appear on the list? As I never got any feedback,
I was wandering if it got lost.

Thank you

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

On Thu, Jul 5, 2012 at 2:49 PM, Sidnei Paciornik <sidnei@puc-rio.br>wrote:

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 <http://www.dcmm.puc-rio.br/> - Departamento de Engenharia de
Materiais
PUC-Rio <http://www.puc-rio.br/>

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 <http://www.dcmm.puc-rio.br/> - Departamento de Engenharia de
Materiais - Materials Engineering Department
PUC-Rio <http://www.puc-rio.br/> - 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 <http://www.dcmm.puc-rio.br/> - Departamento de Engenharia de
Materiais - Materials Engineering Department
PUC-Rio <http://www.puc-rio.br/> - 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










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