1. A method for aligning an imaging system having a microscope objective and a multichannel imager, the method comprising: (a) collecting light emitted from a sample on an x-y positioning stage; (b) obtaining an image of the sample along a rotational axis of symmetry of the microscope objective; (c) calculating a first angle between the multichannel imager and the sample around the rotational axis of symmetry; (d) calculating a second angle between the sample and the x-y positioning stage around the axis of rotational symmetry; (e) rotating the sample by the second angle to align the sample with the x-y positioning stage; and (f) rotating the multichannel imager by the sum of the first angle and the second angle to align the camera with the x-y positioning stage.