Cloning cells after gene editing is a labor-intensive process due to issues around cell viability, clonality and overall cell culture efficiency. The CellRaft AIR SystemAn all-in-one platform for imaging, identifying, and isolating viable single cells, colonies, or organoids using CellRaft Arrays and software-guided selection with CellRaft Cytometry. More provides an imaging-based workflow which supports single cell viability and allows independent clonal colony growth in a matter of days instead of months. The System also supports imaging-based phenotyping prior to isolation of single cells and clonal colonies for CRISPR screening applications.