Integrated device with external light source for probing detecting and analyzing molecules

A system comprising:

• an instrument having
• an excitation energy source configured to emit at least one excitation energy;
• at least one alignment component configured to align an integrated device to the instrument;
• the integrated device having:
• a pixel region having a plurality of pixels, each pixel having:
• a sample well configured to receive a sample;
• and
• at least one excitation-coupling structure configured to direct excitation energy to a vicinity of the sample well;
• and
• at least one waveguide configured to optically couple excitation energy to multiple pixels of the plurality of pixels, and wherein the at least one excitation-coupling structure of each pixel of the multiple pixels is positioned to optically couple with the at least one waveguide;
• and
• an excitation source coupling region for receiving excitation energy from the excitation energy source and coupling the excitation energy into the at least one waveguide.