“…To date, assays of neural organoid connectivity and neuronal activity have not typically been performed in situ ; electrophysiology, calcium imaging and immunofluorescence techniques are generally performed in either slice culture or using dissociated and re-plated organoids (Mariani et al, 2015; Paşca et al, 2015; Qian et al, 2016). Combining advanced optical techniques, such as two-photon microscopy (Truong, Supatto, Koos, Choi, & Fraser, 2011) and light-sheet microscopy (Ahrens, Orger, Robson, Li, & Keller, 2013) with approaches such as optical clearing for immunofluorescence analysis (Azaripour et al, 2016; Chung & Deisseroth, 2013; Renier et al, 2014) will provide a level of analysis in whole intact 3D neural organoids as recently demonstrated (Rigamonti et al, 2016). Moreover, organoid analyses using advanced genetically encoded indicators (Hochbaum et al, 2014) or reporter cell lines driven by cell type specific promoters (Shcheglovitov et al, 2013), together with in situ gene expression analysis (Lee et al, 2015) and connectivity mapping (Cai, Cohen, Luo, Lichtman, & Sanes, 2013; Markram et al, 2015) will also greatly benefit phenotyping.…”