A method for selectively analyzing a sample for viable cells and nonviable cells, comprising: providing a sample comprising a three-dimensional micro-tissue formed of a plurality of one or more viable cells and/or one or more nonviable cells in a cell culture device comprising at least one optically flat window; culturing the one or more viable cells in the sample under cell culture conditions; contacting the sample with a membrane-permeable fluorescent dye and a membrane-impermeable fluorescent quenching dye, the contacting effective to cause: the one or more viable cells and/or the one or more nonviable cells to be dyed by the membrane-permeable fluorescent dye, and the one or more nonviable cells to be dyed with the membrane-impermeable fluorescent quenching dye, the membrane-permeable fluorescent dye characterized by a first fluorescent excitation band and a first fluorescence emission band and the membrane-impermeable fluorescent quenching dye characterized by a second fluorescent excitation band and a second fluorescence emission band; and illuminating the sample under conditions effective to cause: emitting of the first fluorescence emission band from the one or more viable cells dyed by the membrane-permeable fluorescent dye, emitting of the second fluorescence emission band from the one or more nonviable cells dyed by the membrane-impermeable fluorescent quenching dye, and quenching of at least a portion of fluorescence of the membrane-permeable fluorescent dye in the one or more nonviable cells by the membrane-impermeable fluorescent quenching dye; and selectively analyzing the sample for: a presence of the one or more viable cells according to the first fluorescence emission band and/or a presence of the one or more nonviable cells according to the second fluorescence emission band, wherein the selectively analyzing the sample comprises conducting fluorescence imaging microscopy of the sample through the at least one optically flat imaging window. providing a sample comprising a three-dimensional micro-tissue formed of a plurality of one or more viable cells and/or one or more nonviable cells in a cell culture device comprising at least one optically flat window; culturing the one or more viable cells in the sample under cell culture conditions; contacting the sample with a membrane-permeable fluorescent dye and a membrane-impermeable fluorescent quenching dye, the contacting effective to cause: the one or more viable cells and/or the one or more nonviable cells to be dyed by the membrane-permeable fluorescent dye, and the one or more nonviable cells to be dyed with the membrane-impermeable fluorescent quenching dye, the membrane-permeable fluorescent dye characterized by a first fluorescent excitation band and a first fluorescence emission band and the membrane-impermeable fluorescent quenching dye characterized by a second fluorescent excitation band and a second fluorescence emission band; and illuminating the sample under conditions effective to cause: emitting of the first fluorescence emission band from the one or more viable cells dyed by the membrane-permeable fluorescent dye, emitting of the second fluorescence emission band from the one or more nonviable cells dyed by the membrane-impermeable fluorescent quenching dye, and quenching of at least a portion of fluorescence of the membrane-permeable fluorescent dye in the one or more nonviable cells by the membrane-impermeable fluorescent quenching dye; and selectively analyzing the sample for: a presence of the one or more viable cells according to the first fluorescence emission band and/or a presence of the one or more nonviable cells according to the second fluorescence emission band, wherein the selectively analyzing the sample comprises conducting fluorescence imaging microscopy of the sample through the at least one optically flat imaging window.