The increased interest in algae as feedstock for biofuel and high value chemicals, has accentuated the need for a more in-depth study of algal cells at the single cell level. Droplet microfluidics has been established as a multifunctional platform, with many advantages for the study of biological systems in the microscale. In this thesis, droplet microfluidic technology was used to optimise and expand the application of a platform designed for the study and screening of single algal cells. Single Phaeodactylum tricornutum (Pt) cells were encapsulated in microdroplets and their growth was monitored over 11 days and was found to be heterogeneous. To limit cell sedimentation during encapsulation and to increase the time over which the encapsulation procedure could be run, 10% v/v OptiPrep density matching medium was added to the cell suspension prior to the encapsulation. A fluorescence-activated droplet sorting platform was used to detect the fluorescence of encapsulated algal cells. Following modifications to the optics of a previously used platform, the fluorescence measurement uncertainty was reduced from 87% to 8%. This improved platform was used to detect the chlorophyll fluorescence of encapsulated Pt and Ng (N. gaditana) cells, confirming that the screening of cells of different sizes and shapes is possible. Chlorophyll fluorescence sorting was used to isolate droplets containing cells from empty droplets to overcome the issue of the random encapsulation of the cells in droplets. There were no false negatives during the sorting procedure, minimising the loss of cells. GFP fluorescence detection was used to sort GFP-expressing Pt cells from a mixture with wild type cells. Furthermore, droplet sorting was combined with droplet dispensing to collect single GFP-expressing cells and obtain monoclonal cell cultures. Single droplet dispensing enables the screening of mutagenized libraries of cells and the selection of potentially rare cell clones, which is much harder to achieve using other selection methods. To screen cells based on their lipid content, Pt cells encapsulated in microdroplets were stained with BODIPY 505/515. The diffusion of the dye to and from the droplets was studied by fluorescence imaging. Furthermore, the BODIPY 505/515 fluorescence of the droplets was detected with the laser-induced fluorescence detection platform. Several experimental parameters were modified to reduce the high fluorescence background caused by the dye dissolved in the oil surrounding the droplets. A new cell staining method was developed using micelle/hydrogel composite beads loaded with BODIPY 505/515 for dye delivery. The success of this method was assessed with fluorescence microscopy and flow cytometry. The flow cytometry results showed that Pt cells could be stained by these beads within 30 minutes and that the beads could also stain other types of cells, such as Ng cells. The cells could still grow after the staining. The beads were co-encapsulated with Pt cells in microdroplets to test whether this was a viable solution to the issue of leakage of BODIPY 505/515 from the droplets over time. With the microfluidic platform established and optimised, it is now possible to transition from mainly proof-of-concept experiments on algal cell fluorescence detection, to targeted experiments aimed towards answering specific biological questions.