“…Thus the last decades saw the development of a vast number of methods for creating 3D information of cell, tissue, and organ morphology, 3D information of gene expression and gene product patterns, or both. Examples for techniques capable of analyzing small specimens, such as tissue samples or embryos are: in vivo microscopy [7][8][9][10], microcomputed tomography ( CT) [11][12][13], micro-magnetic resonance imaging ( MRI) [9,[14][15][16][17][18], ultrasound biomicroscopy (UBM) [19][20][21], optical projection tomography (OPT) [22,23], confocal microscopy [24][25][26][27][28], atomic force microscopy [29][30][31], 3D electron tomography [32,33], histological or macroscopic section based 3D reconstruction methods [34][35][36][37][38], and 3D episcopic imaging methods (see below). This paper does not compare all the different methods for volume data generation and gene expression analysis.…”