2025MNRAS.542..128B

Ly$\alpha$ emission is key to understanding the process of cosmic reionization. JWST is finally enabling us to measure Ly$\alpha$ emission deep into the epoch of reionization for an increasing number of galaxies. However, discrepancies between measurements of Ly$\alpha$ equivalent widths (EW$_0$) of Ly$\alpha$ emitters (LAEs) have been noted between JWST and ground-based facilities. We employ SPICE, a suite of radiation-hydrodynamical simulations featuring different stellar feedback models, and investigate the impact of radiative transfer effects (e.g. extended emission, Ly$\alpha$-UV spatial offsets) and observational systematics (such as slit placement) on the measured Ly$\alpha$ EW$_0$. We perform radiative transfer of Ly$\alpha$ and UV photons for SPICE galaxies to mimic slit spectroscopy for ground-based slits and JWST-MSA pseudo-slits. We find that spatial Ly$\alpha$-UV offsets exist independently of feedback model, and are common ($>70$ per cent galaxies with $M_* > \rm 10^8 M_\odot$) with median values of $\approx 0.07-0.11\, \rm arcsec$. The theoretical predictions from SPICE are consistent with the observed spatial offset distribution. In addition, spatial Ly$\alpha$-UV offsets are identified as a major cause of loss of flux for JWST-MSA type observations, with median pseudo-slit losses of $\approx 65$ per cent, and $\approx 30$ per cent cases suffering from $>95$ per cent pseudo-slit losses. Even in the absence of such spatial offsets, the presence of extended emission can cause median pseudo-slit losses of 40 per cent, with 4 per cent cases suffering from $>95$ per cent pseudo-slit losses. Finally, complex galaxy morphologies or misplaced JWST-MSA pseudo-slit can lead to underestimated UV continuum, resulting in spuriously high estimates of EW$_0$ from JWST in $6-8$ per cent of galaxies. We compare the predictions from SPICE to a sample of 25 galaxies with Ly$\alpha$ emission observations from both the ground and from JWST. The EW$_0^{\tt JWST}$ and the EW$_0^{\tt Ground}$ exhibit scatter in line with predictions from SPICE, indicating that both physical and systematic effects are likely at play.