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Re: [Seg3D] Layer management, sublayering, and multiple exports

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  • From: Ayla Khan <>
  • To:
  • Subject: Re: [Seg3D] Layer management, sublayering, and multiple exports
  • Date: Fri, 30 Jan 2015 00:37:46 -0700

Hi Paul,

I'm glad to hear Seg3D has been useful for your work.

Both of these are very good ideas, and it would be interesting to try out
different layout options in the layer manager view. We don't have batch
export through the user interface, but should be not too difficult to add.
I've created feature requests for both these items.

If you're willing to try the Python interpreter embedded in Seg3D, you could
try to batch export your segmentations that way. The command is
exportsegmentation, and an example of how to call it to export a segmentation
in a mask layer as a Nrrd file is:

file_path='/Volumes/scratch/misc_data', extension='.nrrd', exporter='')

Or the exporter type can be explicitly given:

file_path='/Volumes/scratch/misc_data', extension='.nrrd', exporter='[NRRD

The layers parameter requires a layer id ('layer_25' in this case). Layer ids
and other useful variables can be found in the Controller Window under the
State Variables tab. Please let me know if you'd like more information about
using the Python interface to automate Seg3D tasks, and thanks for the
feature suggestions.


On Jan 26, 2015, at 9:16 AM, Paul Holcomb wrote:

> Hello Seg3D team! This is Paul Holcomb, West Virginia University graduate
> student and alumnus from the 2014 IBBM course. I have been busy converting
> all of my fellow segmenters and modelers over to Seg3D, and it's been a
> great asset to us in segmenting and analyzing our EM data.
> In our data sets, we tend to deal with multiple masks for a single object
> -- for example: the nucleus, cell body, and organelles of a single cell.
> In the future, it would be handy to have sublayering options in the layer
> manager so that we can better organize these layers under a single "master"
> header for each cell.
> Also, I find myself needing to export multiple segmentations at one time.
> Is there a method for batch export that I'm missing, or is this something
> that could be addressed in future releases?
> Thanks for your time!
> Best wishes,
> Paul Holcomb
> --
> "Hope is a state of mind, not of the world. Hope, in this deep and powerful
> sense, is not the same as joy that things are going well, or willingness to
> invest in enterprises that are obviously heading for success, but rather an
> ability to work for something because it is good." ~Vaclav Havel

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