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Cosmic rays are a global source of ionisation, and the ionisation fraction represents a fundamental parameter in the interstellar medium. Ions couple to magnetic fields, affect the chemistry, and the dynamics of star-forming regions as well as planetary atmospheres. However, the cosmic-ray ionisation rate represents one of the bottlenecks for astrochemical models, and its determination is one of the most puzzling problems in astrophysics. While for diffuse clouds reasonable values have been provided from H$_3^+$ observations, for dense clouds, due to the lack of rotational transitions, this is not possible, and estimates are strongly biased by the employed model. We present here an analytical expression, obtained from first principles, to estimate the cosmic-ray ionisation rate from observational quantities. The theoretical predictions are validated with high-resolution three-dimensional numerical simulations and applied to the well known core L1544; we obtained an estimate of $ζ_2 \sim 2-3 \times 10^{-17}$ s$^{-1}$. Our results and the analytical formulae provided represent the first model-independent, robust tool to probe the cosmic-ray ionisation rate in the densest part of star-forming regions (on spatial scales of $R \leq 0.05$ pc). An error analysis is presented to give statistical relevance to our study.