Data Segmentation:

Image volumes were manually segmented using Amira or Avió. Identifiable anatomy was "painted" and named (labeled) in each plan of the image volume. Anatomical labels are stored in as separate image file (LabelFile (.Labels.am) with the same spatial dimensions as the MRI data. The LabelFile is an image file with a text header containing the label names and numerical identifiers for each label.

Atlas Delivery:

Labels are extracted from the .Labels.am files using MBAT while the label image is exported from Amira as a NifTI (.nii) file. The MRI data, label image and .ilf are used to assemble an atlas in MBAT. The image files are highly portable and can be viewed in many freely available applications including ImageJ, Fiji, MRIcro.

 

Atlas construction reference sources:

Matthew H. Kaufman, (1994). “The Atlas of Mouse Development”Academic Press, London.

Karl Theiler (1972). "The House Mouse: Atlas of Embryonic Development". Springer-Verlag, New York, Berlin, Hiedleberg, London, Paris, Tokyo

Selected publications:

Dhenain, M., Ruffins, S.W., and Jacobs, R.E. (2001) Three-dimensional digital mouse atlas using high-resolution MRI. Dev. Biol. 232, 458–470.

R.E. Jacobs, Papan, C. Ruffins, S., Tyszka, J.M., and Fraser, S.E. (2003). MRI: Volumetric imaging for vital imaging and atlas construction. Nature Review (September, 2003) SS10-SS16.

S.W. Ruffins, Jacobs, R.E., Fraser, S.E. (2002). Towards a Tralfamadorian view of the embryo: multidimensional imaging of development. Curr. Op. Neurobio. 12, 580-586.