ABSTRACT In multicellular organisms including animals, plants and human beings, stem cells play conserved roles in maintaining themselves undifferentiated but continuously dividing to sustain organ development and body formation. Defects in stem cell function lead to abnormal organ development and diseases. On the other side, unraveling stem cell behavior and regulation can provide effective cell-based therapies including tissue regeneration for human diseases such as neurodegeneration, diabetes, and heart disease. To date, the regulatory mechanisms controlling the initiation, proliferation and termination of stem cell niches are still not fully understood. Here, we propose to determine the cellular and molecular basis underlying stem cell homeostasis using the Arabidopsis shoot apical meristem (SAM) as a model system. Because undifferentiated stem cells in Arabidopsis SAMs are at and near the surface and the living SAMs can maintain sessile during experiments, non-invasive time-lapse live imaging approaches are particularly effective in Arabidopsis, to follow the fate of each stem cell and their derivatives and to quantify cell dynamics in vivo. In addition, great genetic resources in Arabidopsis allow us to quantitatively dissect gene function through using an existing array of mutants with changed SAM sizes and stem cell numbers. Using this system, through a combination of in vivo time-lapse confocal imaging, transient and stable perturbations of gene function, in vitro biochemistry and in silico quantification and modeling approaches, we aim to uncover mechanisms by which a small group of key transcriptional regulators that are excluded from stem cells but determine the identity and activity of the stem cells in the SAMs. Our work will not only define the yet missing molecular linkage and cell-cell communication between differentiated and undifferentiated cells, but also elucidate a regulatory network underlying a cell non- autonomous phenomenon in control of stem cell homeostasis.