IntroductionModern microscopy is an invaluable tool, with advances in resolution, contrast, molecular specificity, speed, and biocompatibility to enable visualization of cellular processes in intact tissues and organisms. The use of endogenously produced multicolor fluorescent proteins (FPs) to label cells has emerged as a versatile approach for cell tracking and lineage tracing during morphogenesis or regenerative processes. 1-3 However, many FP variants have similar excitation and emission properties, making unambiguous separation of signals from multiple reporters challenging. The ability to label with multiple FPs in the same experiment and apply high resolution multidimensional imaging can provide insights into complex biologic processes. 4 Recently, the concept of genetically labeling clonal cell populations via fluorescent proteins of distinct colors has been developed. The initial technology known as the "brainbow" 5 was based on controlled transgene recombination, and successive improvements increased the range of applications. [6][7][8][9] Up to 5 different FP were expressed from a single "MultiLabel" expression plasmid using tandem recombineering induced by a tissue-and stage-specific promoter, resulting in homogeneous cell populations all expressing multiple FPs. 10,11 To date, this approach has not been applied to hematopoiesis because of the lack of a highly hematopoietic stem cell-specific promoter. An alternative strategy, known as "RGB marking" uses lentiviral gene ontology (LeGO) vectors encoding red, green, and blue FPs to transduce multiple cell types and track clones after transfer, 12-14 resulting in fluorescence intensities much brighter than most transgenic FPs, and broad combinatorial color diversity.We took advantage of LeGO vectors constitutively expressing 5FPs to mark hematopoietic stem and progenitor cells (HSPCs) and study the process of hematopoiesis at a clonal level over time and in multiple tissues. HSPCs reside within the BM in a complex niche consisting of osteoblasts, stromal cells, adipose tissue, and vascular structures, crucial for maintenance of self-renewal and modulation of differentiation and death pathways. [15][16][17][18] As BM has been inaccessible to direct observation, the interactions between HSPCs and their microenvironment remains largely uncharacterized in vivo. Recently, we established a methodology to visualize the 3D architecture of intact BM using confocal fluorescence and reflection microscopy. 19 We combine generation of a diverse palette of clone colors via cotransduction of HSPCs with 5FPs LeGO vectors with new imaging and analysis technologies to computationally reconstruct the 3D architecture of tissues at high resolution to depths of 150-300 m, elucidating biologically interesting clonal reconstitution patterns. We demonstrate that confocal imaging can be combined with multiphoton microscopy, revealing complementary information from autofluorescent and second-harmonic-generating (SHG) structures. Furthermore, dynamic 4D high-resolution imaging ...