An optical instrument comprising: a first vertical cavity laser VCL source configured for generating tuned emission over a first wavelength range to generate a first wavelength sweep; and a second VCL source configured for generating tuned emission over a second wavelength range to generate a second wavelength sweep; and an optical system configured for delivering at least a portion of the first wavelength sweep and at least a portion of the second wavelength sweep to a sample; a reference signal generator configured for receiving at least a portion of the tuned emission from the first wavelength sweep to generate a reference signal for the first wavelength sweep and at least a portion of the tuned emission from the second wavelength sweep to generate a reference signal for the second wavelength sweep; and a sample detector configured for detecting tuned emission from the first wavelength sweep that is affected by the sample to generate a sample signal for the first wavelength sweep and tuned emission from the second wavelength sweep that is affected by the sample to generate a sample signal for the second wavelength sweep; and a digitizer subsystem configured for converting the sample signal from the first wavelength sweep into sample digital data for the first wavelength sweep, the sample signal for the second wavelength sweep into sample digital data for the second wavelength sweep, the reference signal for the first wavelength sweep into reference digital data for the first wavelength sweep, and the reference signal for the second wavelength sweep into reference digital data for the second wavelength sweep; and an alignment processor configured for using the reference digital data for the first wavelength sweep and the reference digital data for the second wavelength sweep as input to process the sample digital data for the first wavelength sweep and the sample digital data for the second swept wavelength sweep to generate output digital data, wherein the resulting output digital data is aligned with respect to at least one of: wavelength, wavenumber, and interferometric phase, wherein the alignment processor is configured to compute a correspondence match between a subset of data from the reference digital data for the first wavelength sweep and a subset of data from the reference digital data for the second wavelength sweep, or between a subset of data derived from the reference digital data for the first wavelength sweep and a subset of data derived from the reference digital data for the second wavelength sweep as part of the processing to generate output digital data. a first vertical cavity laser VCL source configured for generating tuned emission over a first wavelength range to generate a first wavelength sweep; and a second VCL source configured for generating tuned emission over a second wavelength range to generate a second wavelength sweep; and an optical system configured for delivering at least a portion of the first wavelength sweep and at least a portion of the second wavelength sweep to a sample; a reference signal generator configured for receiving at least a portion of the tuned emission from the first wavelength sweep to generate a reference signal for the first wavelength sweep and at least a portion of the tuned emission from the second wavelength sweep to generate a reference signal for the second wavelength sweep; and a sample detector configured for detecting tuned emission from the first wavelength sweep that is affected by the sample to generate a sample signal for the first wavelength sweep and tuned emission from the second wavelength sweep that is affected by the sample to generate a sample signal for the second wavelength sweep; and a digitizer subsystem configured for converting the sample signal from the first wavelength sweep into sample digital data for the first wavelength sweep, the sample signal for the second wavelength sweep into sample digital data for the second wavelength sweep, the reference signal for the first wavelength sweep into reference digital data for the first wavelength sweep, and the reference signal for the second wavelength sweep into reference digital data for the second wavelength sweep; and an alignment processor configured for using the reference digital data for the first wavelength sweep and the reference digital data for the second wavelength sweep as input to process the sample digital data for the first wavelength sweep and the sample digital data for the second swept wavelength sweep to generate output digital data, wherein the resulting output digital data is aligned with respect to at least one of: wavelength, wavenumber, and interferometric phase, wherein the alignment processor is configured to compute a correspondence match between a subset of data from the reference digital data for the first wavelength sweep and a subset of data from the reference digital data for the second wavelength sweep, or between a subset of data derived from the reference digital data for the first wavelength sweep and a subset of data derived from the reference digital data for the second wavelength sweep as part of the processing to generate output digital data.