The invention relates to a micro-reactor for observing small particles, cells, bacteria, viruses or protein molecules in a fluid. The micro-reactor shows a first channel formed between two layers for containing the fluid, with an inlet and an outlet, the two layers separated by a first distance. A likewise second channel with an inlet and an outlet is placed adjacent to the first channel. A gap connects the first channel and the second channel, at the gap at least one layer showing a window transparent to the method of inspection and at the window the two layers being separated by a very small distance of, for example, 1 μm or less.The micro-reactor may be used with an optical microscope (in which all particles are in focus), inspection with a Scanning Transmission Electron Microscope (in which the range of the electrons is limited), inspection with soft X-rays in the 250-500 eV range (also showing a limited range), etc. A method of using the micro-reactor includes applying a gradient over the gap, thereby causing the particles to cross the gap. The gradient may be static or dynamic, and may be a gradient in concentration, of a chemical or biological material, in pressure, in temperature, in electric potential, or in magnetic field. By detecting a property of the particles upstream in the first channel, e.g. using fluorescent labels on the particles, and then applying a pressure burst over the channels when the property meets certain preset criteria, only selected particles can be placed in the gap.