An optical instrument comprising: a set of N VCL sources configured for generating tuned emission over N wavelength ranges to generate N wavelength sweeps, where N is a number ranging from 2-6; an optical system configured for delivering at least a portion of each of the N wavelength sweeps to a sample; a reference signal generator configured for receiving at least a portion of each of the N wavelength sweeps to generate N reference signals; a sample detector configured for detecting tuned emission affected by the sample to generate N sample signals; a digitizer subsystem configured for converting the N sample signals from the N wavelength sweeps into sample digital data for the N wavelength sweeps and converting the N reference signals for the N wavelength sweeps into reference digital data for the N wavelength sweeps; and an alignment processor configured for using the reference digital data for the N wavelength sweeps as input to compute a set of alignment parameters and process the sample digital data for the N wavelength sweeps to generate output digital data, wherein the output digital data is aligned using the set of alignment parameters previously computed as input, wherein the output digital data is aligned with respect to wavelength, wavenumber, or interferometric phase; wherein the aligning the output digital data comprises: using a first subset of data including a first number of samples of the reference digital data for the N wavelength sweeps to form a template signal; using a second subset of data including the first number of samples of the sample digital data for the N wavelength sweeps with an offset value to form a comparison signal; searching for the offset value that aligns the template signal to the comparison signal based on a minimizing or maximizing a quality metric. a set of N VCL sources configured for generating tuned emission over N wavelength ranges to generate N wavelength sweeps, where N is a number ranging from 2-6; an optical system configured for delivering at least a portion of each of the N wavelength sweeps to a sample; a reference signal generator configured for receiving at least a portion of each of the N wavelength sweeps to generate N reference signals; a sample detector configured for detecting tuned emission affected by the sample to generate N sample signals; a digitizer subsystem configured for converting the N sample signals from the N wavelength sweeps into sample digital data for the N wavelength sweeps and converting the N reference signals for the N wavelength sweeps into reference digital data for the N wavelength sweeps; and an alignment processor configured for using the reference digital data for the N wavelength sweeps as input to compute a set of alignment parameters and process the sample digital data for the N wavelength sweeps to generate output digital data, wherein the output digital data is aligned using the set of alignment parameters previously computed as input, wherein the output digital data is aligned with respect to wavelength, wavenumber, or interferometric phase; wherein the aligning the output digital data comprises: using a first subset of data including a first number of samples of the reference digital data for the N wavelength sweeps to form a template signal; using a second subset of data including the first number of samples of the sample digital data for the N wavelength sweeps with an offset value to form a comparison signal; searching for the offset value that aligns the template signal to the comparison signal based on a minimizing or maximizing a quality metric. using a first subset of data including a first number of samples of the reference digital data for the N wavelength sweeps to form a template signal; using a second subset of data including the first number of samples of the sample digital data for the N wavelength sweeps with an offset value to form a comparison signal; searching for the offset value that aligns the template signal to the comparison signal based on a minimizing or maximizing a quality metric.