Connecting a spectrometer to a microscope for microspectroscopy studies
Spectroscopy investigation of samples on the microscopic scale, incorporating different modalities such as µ-Raman, photoluminescence, TAR and plasmonics, is being more widely used to gain ever more information on samples. The term Microspectroscopy is generally used to cover the ever increasing variations on these techniques. Samples can range from in-vitro and in-vivo tissue samples, quantum structures (dots, wires), material surfaces and crystals.
Task at hand
For many research groups a modular approach [1, 2] can be adopted where spectrometers are coupled either directly or indirectly to their already existing microscopes. Such configurations are relatively straight forward to achieve and typically involve a number of low cost accessories, such as optical fibers for indirect coupling, or adapter flanges, lens relay optics, and wide aperture slits for direct coupling. Direct coupling offers the advantage of being able to relay the image of the sample on the microscope stage through the spectrometer on to the CCD detector. The system can then be used in ‘imaging mode’ to first align and view the sample, and then simply switch to ‘spectroscopy mode’ to acquire spectral data.
Andor provides a range of spectrometers  and detectors (CCD, sCMOS, ICCD, ICMOS) that are widely used in microspectroscopy setups [2, 3]. All the necessary accessories to facilitate such optomechanical coupling are available including the feet and port adapters for all the main microscopes to ensure the correct optical height is achieved between the microscope and the spectrograph. Coupling to both inverted and upright microscopes is possible . In the latter case a table may be used to raise the spectrometer and camera to match the optical height of the top port. Some examples are illustrated below in the pictures and a link to an applications webinar .
Having achieved the optomechanical coupling – the next challenge is the integrated control of the micro-spectroscopy system. Andor has provided a plug-in module for Micro-manager  which allows for software control of the microscope, light sources, filters, xyz stages and, the spectograph and detector. Alternatively these individual sub-systems may be controlled with Solis or via Labview, Matlab, or C++ applications etc, using the Andor SDK.
Examples of microscopes and spectrographs being used in µ-spectroscopy modular setups: