The ever accelerating state of technology has powered an increasing interest in heat transfer solutions and process engineering innovations in the microfluidics domain. In order to carry out such developments, reliable heat transfer diagnostic techniques are necessary. Thermo-liquid crystal (TLC) thermography, in combination with particle image velocimetry, has been a widely accepted and commonly used technique for the simultaneous measurement and characterization of temperature and velocity fields in macroscopic fluid flows for several decades. However, low seeding density, volume illumination, and low TLC particle image quality at high magnifications present unsurpassed challenges to its application to three-dimensional flows with microscopic dimensions. In this work, a measurement technique to evaluate the color response of individual non-encapsulated TLC particles is presented. A Shirasu porous glass membrane emulsification approach was used to produce the nonencapsulated TLC particles with a narrow size distribution and a multi-variable calibration procedure, making use of all three RGB and HSI color components, as well as the proper orthogonally decomposed RGB components, was used to achieve unprecedented low uncertainty levels in the temperature estimation of individual particles, opening the door to simultaneous temperature and velocity tracking using 3D velocimetry techniques.