3D printing technologies have allowed the development of prototypes in several fields, such as clinical, aerospace, and infrastructure, to name a few. Another use is to adapt the laboratory instruments to customized applications to improve experiments and measurements in the data acquisition process. Some equipment is modified to include low-cost cameras, optical components, sensors, and mechanical artifacts using printed accessories employing PLA or PETG filaments, such as telescopes, microscopes, and spectrometers. These accessories allow us to maximize the features of the instruments and reduce the research cost. We describe a semi-automatic method for microalgae counting based on a digital microscope adapted to a 3D printing mechanical support and image processing in Matlab. Calibration will be carried out using a Neubauer chamber but will not be required for measurements, which makes a difference compared to similar methods. The results obtained for micro-algae counting show an average error of less than 5% compared to visual counting conducted by a biochemical specialist. We are describe a simple and low-cost method of counting microalgae using 3D printing technologies. .