Developmental biology investigates how organisms grow and develop, with a focus on cell differentiation, tissue formation, and organogenesis. Zebrafish (Danio rerio) serves as a key model organism due to its transparent embryos and rapid development, allowing real-time observation of developmental processes. Fluorescence and confocal microscopy are commonly used to study labelled proteins, signalling pathways, and organ development at cellular level resolution. Advanced techniques like two-photon and light-sheet microscopy overcome certain limitations of conventional confocal microscopy and allow imaging of live zebrafish embryos in three dimensions, minimizing phototoxicity. Microscopy’s versatility is crucial for understanding the cellular mechanisms underpinning development in zebrafish.

Super resolution (SR) microscopy techniques surpass the diffraction limit, achieving resolutions below 200 nm. These methods utilize advanced strategies like fluorescent molecule localization or selective depletion of excited states to enhance spatial resolution. Super-resolution microscopy is widely applied in cellular and molecular biology to observe subcellular structures, protein interactions, and dynamic processes at a nanoscale level. These techniques have revolutionized our understanding of cellular organization, enabling insights into the molecular mechanisms underlying health and disease.

Different types of microscopy are used in plant biology research. To acquire detailed imaging of plant cells, tissues, and organelles with high resolution and specificity, fluorescent microscopy is often chosen. By using fluorescent dyes or autofluorescence, researchers can observe cell walls, chloroplasts, and other structures in living or fixed samples. This technique is essential for studying cellular processes like photosynthesis, nutrient transport, and cell division. Confocal microscopy allows visualization of complex three-dimensional structures, such as root tips or leaf tissues, and tracking of dynamic processes in response to environmental changes. 

Microscopy is pivotal in research of the worm Caenorhabditis elegans, enabling the visualization of its transparent body and cellular structures. Researchers commonly use brightfield and differential interference contrast (DIC) microscopy to observe its development, behaviour, and anatomy in vivo. Fluorescence microscopy allows detailed imaging of specific cells, tissues, or molecular processes using fluorescent markers. Advanced techniques like confocal microscopy and two-photon microscopy enable three-dimensional visualization of neural networks, intracellular events, and gene expression patterns. Super resolution microscopy reveals nanoscale structures like synapses or protein complexes. These methods are instrumental in studying key biological phenomena, including neural development, aging, and gene function. Additionally, non-invasive live imaging of C. elegans ensures real-time observation of dynamic processes, making microscopy essential for unravelling its biology.

Tissue clearing provides researchers with a tool to investigate intact biological structures in three dimensions. This is achieved by making tissues transparent while preserving their cellular architecture and fluorescence. Tissue clearing removes lipids and other opaque elements, enabling deeper light penetration and clearer imaging. Combined with advanced microscopy techniques like multiphoton or light-sheet microscopy, cleared tissue imaging provides detailed views of complex systems, such as neural networks or vascular structures, within whole organs or large tissue sections. It is especially valuable in neuroscience, developmental biology, and pathology, where understanding spatial relationships and large-scale structures is crucial.