Microinjection is a technique in which a foreign material is introduced into the biological cell using micropipettes. Vision sensing and servoing play a crucial role in the automation of various microinjection operations in medical devices. This study proposes a vision-based technique that has been developed towards the automation of microinjection applications. This study provides a comprehensive algorithm that can detect the injection and holding pipette as a part of the injection system and then automatically align them in three orthogonal axes. The tip of the injection pipette was successfully measured at various magnifications. The zebrafish embryo as a biological model is automatically detected and positioned within the field of view (FOV) of the microscope in real-time regardless of its initial position. The algorithm has been examined and verified for the proposed technique to successfully conduct full operations including alignment of the pipettes, detection of the tip position of the injection pipette at various magnifications and positioning the zebrafish embryo to the FOV of the microscope.