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Re: [Seg3D] Mask a label image over the corresponding input image

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  • From: jess <>
  • To: Surojit Saha <>
  • Cc:
  • Subject: Re: [Seg3D] Mask a label image over the corresponding input image
  • Date: Fri, 25 Oct 2019 10:19:44 -0600

Hi Surojit,

It seems like you are trying to save the mask layer and the image layer to
the same file in Seg3D. Although the nrrd format would probably support this
in some way, it isn’t supported in Seg3D. It may be easier to save them out
as individual files and handle them that way.

Also, I’m not sure why you are saving the layers to disk to visualize it in
Seg3D. Once you load the images, they should be visible. Also there is a
mask data filter which will apply a mask to a data layer (in the Data Filters
menu). Perhaps this is what you are looking for?


> On Oct 23, 2019, at 12:52 PM, Surojit Saha <> wrote:
> Hi,
> I use seg3D to visualize NRRD files.
> I wish to apply a masking layer over an image and visualize it in seg3D. I
> tried to realize this by saving the mask information in NRRD format along
> with the original image, but did not succeed.
> From the documentation of seg3D it appears it can but I did not understand
> the mechanism to feel the effect.
> I would appreciate any help to resolve the same.
> Thanks
> Surojit Saha
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