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

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  • From: Kristen Zygmunt <>
  • To:
  • Subject: Re: [Seg3D] Layer management, sublayering, and multiple exports
  • Date: Fri, 30 Jan 2015 10:06:16 -0700

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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