. Author manuscript; available in PMC: 2012 Aug 1.

Published in final edited form as: Conf Proc IEEE Eng Med Biol Soc. 2011 Aug;2011:8086–8089. doi: 10.1109/IEMBS.2011.6091994

Algorithm 1.

Lossless 2-D to 3-D Reconstruction

L1: Start with set of serial 2-D images

L2: Quantify cellular gene expression in L1 images using Celldetekt

L3: Generate artifact mask images from L1 images using Deftekt

L4: Fix tears in L1 images using Deftekt

L5: Compute 2-D image-to-image rigid registration for L4 images

L6: Compute 2-D image-to-image elastic warps for L5 images using bUnwarpJ

L7: Compress L6 volume to isotropic resolution

L8: Use lossless encoding algorithms to apply transformations computed in steps L4 – L7 to L2 images.

L9: Use lossless encoding algorithms to apply transformations computed in steps L4 – L7 to L3 images.