Charged and neutral particles, photons (13), photonic optics, detectors (15) and sensor arrays are used for application to molecular imaging, communication with biological organisms and monitoring and learning biological activity inside living organisms. The living organisms include among others living tissue, biological organs, cells (10), eukaryotes, prokaryotes, viruses and phages. Molecular imaging can be an effective new tool to understand the mechanisms of life and communicate, modify and control it. Techniques, methods and devices are described to achieve these aims. The probes used in molecular imaging described above will include the full spectrum of photons; charged and uncharged particles (13); chemicals; and biological probes.