共軛焦顯微技術被廣泛地應用在研究細胞的立體結構、細胞及組織的物質變化分析、時間變化分析以及濃度分析等方面。在共軛焦顯微技術使用的同時，一些螢光染色物質和標示電位變化或者是鈣離子變化的物質，常常被利用來標示細胞的活動及變化。在藥物的製造與開發上，研究者利用共軛焦顯微技術來偵測藥物對於細胞作用的活性及影響。至於神經科學方面，共軛焦顯微鏡可以清楚地分析神經纖維的微小結構以及物質傳導活動。在遺傳學的研究上，利用嵌入特定螢光蛋白的載體，可以追蹤特殊基因的表現。甚至於在臨床醫學的應用方面，共軛焦顯微技術被用在偵測特殊細胞或者癌細胞的活性及分布情形，還有細胞組織的病理表現、疾病診斷及研究等等。雖然傳統的光學顯微鏡以及電子顯微鏡應用在細胞影像研究上已行之有年，但是共軛焦顯微技術能改善前二者之低解析度以及只能應用在固定後的細胞等限制，以高解析度和即時活體細胞影像攝影的優勢，提供研究者更清晰以及可信賴的研究成果。所以共軛焦顯微技術在生物技術、生物醫學研究以及臨床醫學研究上，提供了一個方便準確又可信度佳的研究工具。

Confocal fluorescence studies provide information on the identity, size, stereo-structure,time-change, substance diffusion, and concentration of fluorescent-labeled substances.Intracellular or membrane-bound fluorescent dyes as well as voltage- and calcium-dependentindicators are all used to investigate the functions and activities of cells. In the pharmaceuticalindustry, confocal microscopy is now a widely applied tool for studying the cellular effects of drugcandidates. For cellular imaging, confocal optics provide a significant improvement in spatialresolution and data quantity. Confocal microscopy is being applied in neurobiology for detectingmicrostructures and activities within neurons. The technique is also used in clinics for diseasediagnoses, in tracing pathological changes, and in studies of angiogenesis under several conditions.Furthermore, researchers in genetics use confocal microscopy to trace the expression of geneticallyencoded fluorescent proteins. The field of live-cell imaging has also greatly benefited fromapplications of confocal microscopy. Future developments in this field will be of great interest andbenefit to both biotechnological and medical research.