Researchers from myriad fields frequently seek to quantify and classify concentrations of carbonaceous aerosols as organic carbon (OC) or elemental carbon (EC). This is commonly accomplished using thermal-optical OC/EC analyzers (TOAs), which enable measurement via controlled thermal pyrolysis and oxidation under specific temperature protocols and within constrained atmospheres. Several commercial TOAs exist, including a semi-continuous instrument that enables on-line analyses in the field. This instrument employs an in-test calibration procedure that requires relatively frequent calibration. This article details a calibration protocol for this semi-continuous TOA and presents an open-source software tool for data analysis and rigorous Monte Carlo quantification of uncertainties. Notably, the software tool includes novel means to correct for instrument drift and identify and quantify the uncertainty in the OC/EC split point. This is a significant improvement on the uncertainty estimation in the manufacturer's software, which ignores split point uncertainty and otherwise uses fixed equations for relative and absolute errors (generally leading to underestimated uncertainties and often yielding non-physical results as demonstrated in several example data sets). The demonstrated calibration protocol and new software tool enabling accurate quantification of combined uncertainties from calibration, repeatability, and OC/EC split point are shared with the intent of assisting other researchers in achieving better measurements of OC, EC, and total carbon mass in aerosol samples. Video Link The video component of this article can be found at https://www.jove.com/video/59742/ 1) have been suggested to be the key component of PM responsible for adverse health effects and outcomes 2,3,4. Particulate carbon in the atmosphere is a critical climate pollutant, where different carbonaceous species are known to have variable, even opposite, impacts. Black carbon is potentially the second strongest direct radiative forcer in the earth's atmosphere 5,6,7,8. When deposited on snow and ice, black carbon also reduces the reflectivity of the arctic landscape, enhancing the absorption of sunlight, and increasing the rate of melt 9,10,11,12. Contrastingly, hygroscopic organic carbon particles act as cloud condensation nuclei, increasing the mean reflectivity of earth, and causing a cooling effect 13. Accurate classification of sampled carbonaceous material and concurrent quantification of measurement uncertainties are thus essential aspects of particulate matter measurements. Differentiating between organic and elemental carbon in a particulate-laden sample can be achieved using a thermal-optical analysis 14. Commercial, laboratory-based systems for thermal-optical carbon analyses have been created 15,16,17 including an on-line, semi-continuous analyzer 18 that enables the execution of thermal-optical analyses in the field. The present work describes a detailed procedure for calibrating this latter OCEC instrument (see Table of Materials) ...