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Re: [Seg3D] Exporting segmentation out of original bounds

Chronological Thread 
  • From: Jess Tate <>
  • To:, Sander Land <>
  • Subject: Re: [Seg3D] Exporting segmentation out of original bounds
  • Date: Mon, 8 Feb 2016 11:10:40 -0700

Hi Sander,

The 2D viewer will be bound by the label that is highlighted (blue), so that if you have the original volume highlighted, you won't be able to see slices of the extended volume.  By changing selected layers as needed, you should be able to see every slice of every volume.  

exporting and importing into matlab can be a bet tricky, as it will depend on your reader in matlab for the nrrd format.  Make sure that it accounts for the spacing and origin and then make sure that the functions you are using do the same.  What happens when you try to reload it into Seg3D?

There are a few tools in Seg3D for resizing a volume, such as the resampling tool, transform tool, and the crop tool.  extending the grid, ie, padding a volume, is not yet a tool in Seg3D, but can be done using the python console.  I will attach a python function that you can use.  To use this code, open the python console in Seg3D (from the Window menu) and type the foloowing (you cannot paste multiple lines):


The padding script takes the filename of the volume to pad (must be a nrrd),  the filename without extension to save the output, and the padding parameters for each direction. The example above will pad the volume by 10 voxels, adding 20 voxels in each direction.  


import os
import threading

def padding(segFilename, outputpath, pad_level,type):
  if not os.path.exists(segFilename):
    raise ValueError("Path %s does not exist." % segFilename)

  if type=='segementation':
    layers = importlayer(filename=segFilename, importer='[Teem Importer]', mode='label_mask')
  elif type=='scan':
    layers = importlayer(filename=segFilename, importer='[Teem Importer]', mode='data')
    raise ValueError("input type  %s not recognised." % type)

# get dimensions from group.  this only  works if the layers are in the first group loaded
# TODO: find a way to access groupid from layerid.
  dims= get(stateid='group_0::dimensions')


  new_dims=[dims[0]+2*pad_level[0], dims[1]+2*pad_level[1],dims[2]+2*pad_level[2]]

  if data_loc=='node':


# this list is used to combine all the layers into a single data layer for exporting.
# this implementation is dependant on the order of the layers, 
# which is a problem because seg3D currently preserve the order of layers when loaded.

  if type=='segmentation':
    if len(padded)>26:
      raise ValueError("Too many layers to use in this operation." % len(padded))
    express='[RESULT = (A==1)*1'

    for k in range(1,len(padded)):
      tmp_exp=' + (' + alpha[k] + '==1)*' + str(k+1)
    express=express + ';]'

  elif type=='scan':


  result=exportlayer(layer=grayscale,file_path=outputpath,exporter='[NRRD Exporter]',extension='.nrrd')
  print('file saved to '+outputpath)

def wait_for_layer(layer):

#checks to make sure that the layer is available before trying operations on it.

  c = threading.Condition()
  layerStatus = get(stateid=layer+"::data")
  counter = 1
  with c:
    while not layerStatus == "available":
      if counter > MAX_ITERATIONS:
      counter += 1
      layerStatus = get(stateid=layer+"::data")
      print('wainting for '+layer)

On Feb 8, 2016, at 4:56 AM, Sander Land <> wrote:

Hi Jess,

Somebody else created the project, and I'm not even sure how they got bits to be outside the image volume. Going back to the original project it looks like "mask layer -> transform". The "X" slice view does not go down further than the original volume either. Exporting to .nrrd and reading that in matlab has the same result as exporting to matlab.
I think the exporter is confused about the two layers not being aligned, but  I'd sort of expect the export function to export what I see on the screen regardless.
Anyway, starting over I don't see any options for extending or resizing a grid, where can I find this?


On Fri, Feb 5, 2016 at 7:18 PM, Jess Tate <> wrote:
Hi Sander,

There may be a couple of things going on here.  The simplest thing to check is to make sure that you are exporting and importing the right layers.  to create the segmentation 'out of bounds'  you needed to expand the grid, which it seems that you did.  Then you need to copy the entire layer to the new grid and save out the segementations from those new layers.  You can try right clicking on the desired layer to export it also.  

The matlab format from Seg3D doesn't save the spacial information, if I remember correctly.  That means if you have two volumes of different numbers of elements, one may be shifted depending on where the origin is supposed to be (as matlab will just set it to 0,0,0).  It could also be the wrong size depending on what the relative spacing is supposed to be.  


On Feb 5, 2016, at 4:09 AM, Sander Land <> wrote:

Hi Jess,

I am using File->Export Segmentation. Both 'to matlab' and 'to nrrd' have the same problem.
Here are some screenshots:
Image 1: `cap' visible outside image range.
Image 2: Exporting, see the cap is component 7.
Image 3: viewing in matlab, with hole clearly visible on the left.

As there does seem to be a component 7 in the matlab data, I've tried to see where it ends up, and turns out the problem is even worse than simple omission.
Component 7 gets translated to somewhere else in the volume and intersects with it, as shown here:
(output of figure(1); clf; isosurface( == 1,0.5); hold on; p=patch(isosurface( ="=7,0.5));set(p,'FaceColor','r');" axis equal)


On Thu, Feb 4, 2016 at 4:57 PM, Jess Tate <> wrote:
Hi Sander,

It’s a little tricky to understand what is going on, because when you export a segmentation, it should just save out the entire label mask.  Is it possible you are exporting the original image on accident?  You can try the 'Export Segmentation' option in the file menu, which has more controls than right clicking on the layer and exporting it that way.  If that isn’t working, a screen shot may help determine what is going on.


> On Feb 4, 2016, at 5:05 AM, wrote:
> I have an image data set which is missing a small part due to the bounds of
> the imaging. I've filled this in using the paint tool to make a smooth shape.
> However, when exporting the data set it's cut off again at the original
> bounds. Is there a way to extend these bounds and export the entire
> segmentation?
> Thanks,
> Sander

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