Mask Image for Region of Interest (ROI)

For validating the circuits we would need to specify “regions of interest” for a given atlas (for example, pick a sphere within a layer to measure cell density). A mask image is generated for given specific shape and stored in NRRD format with the following metadata.

Specification

The meta data stored in the NRRD file should follow the specification below:

Field	Value Type	Suggested Value	Comments
dimension	integer	3	dimension of the image is always 3 for volumetric data
encoding	string	gzip	use ‘gzip’ for compressing the data
endian	string	little	use ‘little’ for x86 machines
kinds	list of string	[‘domain’, ‘domain’, ‘domain’]	use ‘domain’ to indicate that the axis is image axis
sizes	list of integer	[{size_x}, {size_y}, {size_z}]	the size of the volume in x, y, z dimension
space directions	3d matrix		A 3D matrix indicating the orientation of the image data, with the value indicating the spacing of the voxel
space origin	list of float	[{origin_x}, {origin_y}, {origin_z}]	physical coordinates of the image origin
space	string	{x_orientation}-{y_orientation}-{z_orientation}	the orientation of the image data, should be consistent with the space direction
type	string	uchar	the type of the values stored in the voxels is unsigned char

Example:

{
  u'space origin': ['-46.540000915527344', '-152.15999984741211', '-152'],
  u'space directions': [['16', '0', '0'], ['0', '16', '0'], ['0', '0', '16']],
  u'sizes': [308, 495, 464],
  u'space': 'left-posterior-superior',
  u'encoding': 'gzip',
  u'endian': 'little',
  u'kinds': ['domain', 'domain', 'domain'],
  u'type': 'unsigned char',
  u'dimension': 3
}