Stem cell fate is influenced by a complex interplay of growth factors, matrices, and mechanical forces, which together create a biochemical and mechanical niche that guides stem cell behavior. This niche includes soluble factors, cell-cell contacts, and cell-matrix adhesions, and is crucial for stem cell survival, self-renewal, and differentiation. Decellularized matrices and synthetic polymer niches are being used in clinical settings to understand how stem cells contribute to tissue homeostasis and repair, such as in fibrotic sites. Multi-faceted technologies are increasingly required to produce and study cells ex vivo, build predictive models, and enhance stem cell integration in vivo for therapeutic benefit. Controlling stem cell trafficking, survival, proliferation, and differentiation in a complex in vivo environment is extremely challenging. Studies show that only a few percent of injected stem cells remain after several days or weeks. Despite this, clinical trials continue, particularly with adult bone marrow-derived mesenchymal stem cells (MSC) for treating non-hematopoietic diseases. While FDA approval for embryonic stem cell-derived cells is a recent milestone, clinical cases highlight technical challenges in soft tissue repair. For example, a patient with ataxia telangiectasia had a stem cell-derived tumor four years after treatment. Stem cells encounter various cues upon implantation, and efforts to understand molecular mechanisms for translation from bench to clinic benefit from new and established technologies. The niche is the in vivo microenvironment that regulates stem cell behavior. Key components include growth factors, cell-cell contacts, and cell-matrix adhesions. In culture, controlling niche interactions in 2D is achieved with micropatterns of extracellular matrix (ECM) islands, which limit diffusion of secreted factors. For human embryonic stem cells (hESC), ECM islands made by microstamping onto a substrate demonstrate minimal island size for maintaining pluripotency. Microfluidic devices control growth factor concentrations, showing a strict inverse relationship between proliferation and differentiation. Cell-cell contacts can influence soluble factor signaling, and micromechanical devices can reversibly move cells into contact. Extracellular matrix not only mediates cell attachment but also binds growth factors, limiting their diffusion. This can be mimicked by synthetically tethering a growth factor to a substrate, which enhances MSC survival and regulates transcriptional networks. Adhesion of MSC and ESC to matrix or other cells is essential for viability. In a study with hESC and muscle-derived stem cells, 576 different combinations of acrylate-based polymers were arrayed to exert wide-ranging effects on cell attachment, proliferation, and lineage induction. For 3D cultures, cross-linked hyaluronic acid hydrogels support hESC growth in undifferentiated masses, possibly due to HA's role in embryonic development. Forces, matrix elasticity, and fibrosis are critical in both in vitro and in vivo settings. Cells generate force and are often exposedStem cell fate is influenced by a complex interplay of growth factors, matrices, and mechanical forces, which together create a biochemical and mechanical niche that guides stem cell behavior. This niche includes soluble factors, cell-cell contacts, and cell-matrix adhesions, and is crucial for stem cell survival, self-renewal, and differentiation. Decellularized matrices and synthetic polymer niches are being used in clinical settings to understand how stem cells contribute to tissue homeostasis and repair, such as in fibrotic sites. Multi-faceted technologies are increasingly required to produce and study cells ex vivo, build predictive models, and enhance stem cell integration in vivo for therapeutic benefit. Controlling stem cell trafficking, survival, proliferation, and differentiation in a complex in vivo environment is extremely challenging. Studies show that only a few percent of injected stem cells remain after several days or weeks. Despite this, clinical trials continue, particularly with adult bone marrow-derived mesenchymal stem cells (MSC) for treating non-hematopoietic diseases. While FDA approval for embryonic stem cell-derived cells is a recent milestone, clinical cases highlight technical challenges in soft tissue repair. For example, a patient with ataxia telangiectasia had a stem cell-derived tumor four years after treatment. Stem cells encounter various cues upon implantation, and efforts to understand molecular mechanisms for translation from bench to clinic benefit from new and established technologies. The niche is the in vivo microenvironment that regulates stem cell behavior. Key components include growth factors, cell-cell contacts, and cell-matrix adhesions. In culture, controlling niche interactions in 2D is achieved with micropatterns of extracellular matrix (ECM) islands, which limit diffusion of secreted factors. For human embryonic stem cells (hESC), ECM islands made by microstamping onto a substrate demonstrate minimal island size for maintaining pluripotency. Microfluidic devices control growth factor concentrations, showing a strict inverse relationship between proliferation and differentiation. Cell-cell contacts can influence soluble factor signaling, and micromechanical devices can reversibly move cells into contact. Extracellular matrix not only mediates cell attachment but also binds growth factors, limiting their diffusion. This can be mimicked by synthetically tethering a growth factor to a substrate, which enhances MSC survival and regulates transcriptional networks. Adhesion of MSC and ESC to matrix or other cells is essential for viability. In a study with hESC and muscle-derived stem cells, 576 different combinations of acrylate-based polymers were arrayed to exert wide-ranging effects on cell attachment, proliferation, and lineage induction. For 3D cultures, cross-linked hyaluronic acid hydrogels support hESC growth in undifferentiated masses, possibly due to HA's role in embryonic development. Forces, matrix elasticity, and fibrosis are critical in both in vitro and in vivo settings. Cells generate force and are often exposed