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[Seg3D] Re: Re: feature request zoom in other views


Chronological Thread 
  • From: Ayla Khan <ayla@sci.utah.edu>
  • To: seg3d@sci.utah.edu
  • Cc: Hon Fai Choi <honfai.choi@gmail.com>
  • Subject: [Seg3D] Re: Re: feature request zoom in other views
  • Date: Tue, 21 May 2013 22:55:27 -0600
Hi Hon Fai,

Segmentations in Seg3D are treated as boolean data, i.e. it keeps track of whether a voxel in the segmentation label mask is "on" or not. When a single segmentation label mask is exported, a value of 1 is assigned using whatever method makes sense for the selected file type. If more than one segmentation label mask is exported in a given file, then the background, or air, is assigned a value of 0, and each label mask is assigned values from 1 onwards.

Now in the case of image stacks, the label masks are passed to an ITK file exporter without modification, which is why the rgb values correspond to the label values (keep in mind that an image stack can contain more than one label mask). It may be possible to alter this to write out label values scaled to the range of grayscale values - this will require some investigation.

Ayla

On May 20, 2013, at 1:37 PM, Alan Morris wrote:

Hon Fai,

The images may look entirely black, but the pixels that are "on" in the segmentation are written with r=1, g=1, b=1, so they look nearly black.  If you open them in a tool such as photoshop, you can adjust them so they are visible.

I'm not sure why segmentations aren't written with the background black and the foreground white.  There may be a reason that I am unaware of.  It could perhaps be a feature request.

Alan


On Sun, May 19, 2013 at 7:10 AM, Hon Fai Choi <honfai.choi@gmail.com> wrote:
Hi Alan,

many thanks you for the tip. I have another question. If I try to
export the segmentation as a image stack (bmp, png or tiff) I only get
black images. Is this a bug or am I doing something wrong?

thank you and with kind regards,
Hon Fai


On Fri, May 17, 2013 at 10:28 PM, Alan Morris
<alan.morris@carma.utah.edu> wrote:
> Hon Fai Choi,
>
> You can zoom in all views in Seg3D.  The controls are just slightly
> different for the 2D viewer.  Try holding SHIFT and right-click while moving
> the mouse up and down.
>
> The 2D viewers require SHIFT because many of the tools utilize the right
> mouse button for other tasks.
>
> Alan
>
>
> On Fri, May 17, 2013 at 4:00 AM, Hon Fai Choi <honfai.choi@gmail.com> wrote:
>>
>> Hi,
>>
>> thank you for making Seg3D available, it is a nice application. I was
>> wondering if you are considering to allow zooming in the views other than
>> the 3D. I am segmenting high resolution images and it would be useful to be
>> able to zoom in to fine tune the segmentation. Will this feature be
>> incorporated soon? If not, would it be difficult to modify this in the
>> source code? I have no experience with interface design or QT.
>>
>> with kind regards,
>> Hon Fai Choi
>
>



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