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

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  • From: "paul.holcomb" <>
  • To: "" <>
  • Subject: Re: [Seg3D] Layer management, sublayering, and multiple exports
  • Date: Fri, 30 Jan 2015 12:07:59 -0500
  • Importance: normal

Nope, that's perfect. Actually ran across that last night. Thanks for the email! 


Sent on the new Sprint Network from my Samsung Galaxy S®4.

-------- Original message --------
From: Kristen Zygmunt
Date:01/30/2015 12:06 PM (GMT-05:00)
Subject: Re: [Seg3D] Layer management, sublayering, and multiple exports

From File->Export Segmentation, you should be able to select multiple mask layers at one time to export.  You can then choose to either save them all into a single file or save them all as individual files.  Is this what you need, or do you need some other functionality?

On Jan 30, 2015, at 12:37 AM, Ayla Khan <> wrote:

> 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:
>  exportsegmentation(layers='layer_25',  file_path='/Volumes/scratch/misc_data', extension='.nrrd', exporter='')
> Or the exporter type can be explicitly given:
>  exportsegmentation(layers='layer_25', file_path='/Volumes/scratch/misc_data', extension='.nrrd', exporter='[NRRD Exporter]')
> 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.
> Ayla
> 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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