Inappropriate wound healing represents a considerable medical challenge associated with high mortality. However, improving on current wound healing therapies has proven difficult due to the complex and dynamic wound environment. The complexity of the wound healing process also puts high demands on the animal models used in wound research, since ideally such models should encompass the full complexity of the wound healing process, and at the same time be accessible for advanced biomedical analysis methods. In this thesis, the aim was to further develop the use of zebrafish embryos in wound healing research. Key advantages of zebrafish embryo models are the ability to visualize complex biological processes in high detail in intact tissues, as well as highly tractable genetics. The first part of the work describes the development of a zebrafish embryo model for investigating the immunomodulatory properties of hydrogels derived from decellularized extracellular matrix (ECM). The results demonstrate that the hydrogels can be properly injected into the embryos and that the host-materials interactions can be explored in detail inside live zebrafish embryos during wound healing. This constitutes a new in vivo model for investigating immunomodulatory materials in a realistic wound healing context. The second part of the work describes the development of a confocal Raman spectrometry imaging (cRSI) method for biomolecular characterization and the study of biological processes in zebrafish. This represents a new imaging modality that enables simultaneous inspection of a multitude of biomolecules in a label-free manner. The use of cRSI was demonstrated for biomolecular discrimination of mycobacteria in a zebrafish infection model, and for live in vivo imaging of zebrafish during the early wound response. Taken together, the work in this thesis has provided a new methodologies and insight for the use in zebrafish embryo models in wound healing research.