We report observations of the high (R$sim$18000) and medium (R$sim$5900) resolution, near-infrared spectra of Jupiters polar regions with the GNIRS instrument at the Gemini North telescope. The observations correspond to the area of main auroral oval in the South and the main spot of the Io footprint in the North. We detected and assigned 18 emission lines of the H$_{3}^{+}$, 2$ u_{2}rightarrow 0$ overtone band in the region from 4800 to 4980 cm$^{-1}$ and 5 additional lines in the extended low-resolution spectrum. We use our new modelling scheme, ATMOF to remove telluric absorption bands of CO$_2$ that feature strongly in the 2 $mu$m region. The H${_2}$ 1-0 S(1), S(2) and S(3) emission lines are also detected in the observed spectral region. We found the rotational temperature and column density of H$_{3}^{+}$ emission at the peak intensity for both northern and southern auroral regions to be the same within the measurement errors (T$_{rot} sim950$K and N(H$_{3}^{+}$) $sim$ 4.5$times10^{16}$m$^{-2}$). The estimates of T$_{rot}$ from H$_{2}$ are consistent within much higher uncertainties with temperatures derived from H$_{3}^{+}$ emissions. We derived the profiles of the H$_{3}^{+}$ emissivity and ion density for both auroral regions providing the first such measurement for the emission associated with the main spot of the Io footprint. We also found a number of weaker lines in the high-resolution spectra that could be associated with emission from high excitation levels in neutral iron, which could be deposited in Jupiters atmosphere as a result of meteor ablation.
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