UV Light can be used to disinfect the material flowing in tubes. Infrared laser light can be used to heat specific particles/cells/droplets if the tube is made from glass. Here is a market report on UV disinfection equipment. A company active in UV disinfection is  uvo3. Transparent polygon scanning can be used in vibrometery, which can be used to measure fluid flows in glass tubes using laser doppler velocimetry. Laser galvo scanning interferometry can be used for flow velocity measurements through disturbing interfaces. Likewise a transparent polygon scanner can be used to measure flow in chemical processes.

Ideally, the glass tube is square to minimize a lensing effect.

Furthermore, an interesting option would to polymerize particles in the tube, or sintering takes place in the tube.  MIT patented this process in US7709554, but used a DMD projector and not a transparent polygon scanner. In addition, I claim the case the walls of the tube are created from Teflon AF. This could for instance done on a micro-fluidic chip which would again be produced by a transparent polygon scanner. One could simply use the setup outlined here and use a transparent polygon instead of a galvo scanner. If this is not sufficient I would make the tube square and sufficient porous by laser engraving the tube with a transparent polygon scanner and  C02 laser, where i spin the prism at a relatively low speed and possibly use an auxiliary bundle to fix the timing.

The speckle pattern can be measured which is created by shining in the tube. This process can for example be is used in the food industry to measure the dairy viscosity in a glass tube. You could walk around in the garden with a handheld Hexastorm and measure the biological status of a plant.
The detector could be a CCD/CMOS camera at the same side or opposite side of the plant leaf or glass tube. Possibly, the transparent polygon scanner is under an angle so the reflected light does not fully transmit back to the polygon scanner but can be measured by another device at the same edge of the tube, like a CMOS/CCD chip/grating light valve with appropriate lens.

The laser is pulsed and the time of flight is measured. This allows one to both record the amplitude and time phase spectrum of the material under measurement.  Incidentally, I claim that gasses are flowing in the tubes or that that tracers are applied to the particles in the tube.