Ultraviolet (UV) auroral emissions on Jupiter offer a unique window into the coupling between the planet's magnetosphere and upper atmosphere. Color ratios derived from molecular hydrogen emissions provide valuable diagnostics for the energy of precipitating electrons and the structure of the auroral atmosphere. We aim to characterize the horizontal and vertical variability of hydrocarbon absorption in Jupiter’s auroral atmosphere using UV data from the Juno-UVS spectrograph and to investigate potential departures from the expected structure. We constructed color ratio maps sensitive to CH₄ and C₂H₂ absorptions for two of Juno’s close approaches to Jupiter, perijoves (PJs) 6 and 10, by integrating auroral H₂ emission over hydrocarbon-sensitive spectral intervals. For CH₄, we redefined the absorbed spectral band, replacing the traditionally used 125–130 nm interval with 135–140 nm to mitigate higher order calibration issues. In regions of intense auroral brightness, we developed a correction method to account for spectral distortion due to detector nonlinearities at high fluxes. The CH₄ and C₂H₂ absorptions generally follow the expected vertical distribution, with the CH₄ density extending to higher altitudes than C₂H₂. However, several localized regions show unexpected spatial distribution of the absorption. In PJ6, such anomalies are attributed to instrumental nonlinearities. Following the correction, the CR distributions become consistent with standard hydrocarbon vertical distributions. In PJ10, however, some anomalous patterns persist despite the correction. Spectral modeling studies indicate that these can be explained by modifying the relative abundances of CH₄ and C₂H₂, suggesting horizontal compositional variability and possible deviations in the homopause altitude between species. Our results confirm that hydrocarbon absorption in Jupiter’s aurora is vertically stratified, but that the altitude of this stratification itself varies horizontally with latitude and longitude. These findings underscore the importance of accounting for local atmospheric composition when interpreting UV auroral spectra and retrieving electron energy distributions. Juno-UVS thus provides a powerful diagnostic for probing both the auroral precipitation and upper atmospheric structure. The framework developed here enables more accurate retrievals of electron energies and provides new constraints on the spatial variability of Jupiter's upper atmosphere. A systematic application to the full Juno dataset will offer deeper insights into the temporal and spatial dynamics of the Jovian aurora.
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