In our core facility we aim to help researchers to maximize the use of wide flow cytometry and bioimaging tools in their studies. In this study we collaborated with the group of Benyamin Rosental and explored the function of Hecacorallia immune system under heat stress. In Hexacorallia, Immune activation due to heat-stress is intriguing given its detrimental effect on corals. Previous gene expression research on coral heat stress induced bleaching found that different immune genes were differentially regulated and suggested immune activation. The cellular mechanisms of immunity involved in coral bleaching is currently unknown, and it is still not understood if immune response is a consequence of bleaching or is directly affected by the heat stress itself. To address this question, we used various flow cytometry and bioimaging based assays. We developed a research pipeline that facilitate the translation of gene expression data to a deep understanding of the immune system function in Hexacorallia under acute heat shock. Our study is a first step in understanding the part that the immune response has, if at all, in coral bleaching.