In this thesis a robust Python based software for controlling a Chlorophyll-a Pulse-Amplitude-Modulated (PAM) fluorescence microscope and analysing subsequent data has been developed and validated. The automation software, called PACMan (PAM Automation Control Manager) was made for the purpose of increasing the amount of single cell data generated per experiment. PACMan includes an autofocus algorithm and the ability to vary experimental parameters during experiments. The analysis software, called PAMalysis, processes and facilitates interpretation of PAM experimental data, printing both text files and creating graphical output. PACMan was used on two different phytoplankton species of the Symbiodiniacae family to characterize them under thermal stressors while immobilized on a microfluidic device. The heterogeneity of the phytoplanktons response to increasing thermal stress was evaluated and the best performers under heat stress have been removed using Laser Capture Microdissection for downstream cultivation. PACMan was also used to compare the response of 4 Symbiodiniacae species to increasing relaxation time between light pulses and to image the heterogeneity of response of the common eukaryotic model organism C. reinhartii to a chemical gradient of the common herbicide DCMU (3-(3,4-dichlorophenyl)-1,1-dimethylurea).