16We previously identified and modelled a principle of visual maps alignment in the midbrain 17 involving the mapping of the retinal projections and concurrent transposition of retinal guidance 18 cues into the superior colliculus providing positional information for the organization of cortical V1 19 projections onto the retinal map . This principle relies on mechanisms involving 20 Epha/Efna signaling, correlated neuronal activity and axon competition. Here, using the 3-step 21 map alignment computational model, we predict and validate in vivo the visual mapping defects in 22 a well-characterized mouse model. Our results challenge previous hypotheses and provide an 23 alternative, although complementary, explanation for the phenotype observed. In addition, we 24 propose a new quantification method to assess the degree of alignment and organization between 25 maps, allowing inter-model comparisons. This work generalizes the validity and robustness of the 26 3-step map alignment algorithm as a predictive tool and confirms the basic mechanisms of visual 27 maps organization. Savier and Reber, 56 2018). Several hypotheses have been made to account for the phenotypes observed in mouse 57 genetic models and this extensive body of work has been used to generate computational 58 approaches which attempt to replicate experimental findings 62 Savier et al., 2017). However, until recently, these models have not been able to explain how 63 collicular visual maps are aligned during development. 64Interestingly, the formation of the retino-collicular map occurs prior to the establishment of the 65 cortico-collicular map. Other studies have shown that the existence of the retino-collicular map is 66 necessary for the formation of the cortico-collicular map, suggesting an interdependence of the 67 two mechanisms (Khachab and Bruce, 1999;Rhoades et al., 1985;Triplett et al., 2009). Similar 68 observations have been made in other part of the visual system (Shanks et al., 2016). Another 69 piece of evidence came from the study of map alignment in the Isl2-Epha3KI, one of the best 70 characterized mutant in the field. In these mutants, the Epha3 receptor is ectopically expressed in 71 50% of RGCs, leading to a duplication of the retino-collicular map . Strikingly, 72 a full duplication of the cortico-collicular map is also observed in the Isl2-Epha3 KI/KI homozygous 73 mutants, which display a normal retinotopy in the visual cortex (Triplett et al., 2009). The authors 74 concluded that a retinal-matching mechanism involving spontaneous correlated activity in the 75 retina instructs cortico-collicular projections and alignment onto the retino-collicular map. 76Alternative explanations can also be suggested. For instance, the ectopic expression of Epha3 77 specifically in the retina may alter the expression of other members of Epha/Efna throughout the 78 visual system disrupting maps formation and alignment. In another example, molecular cues 79 originating from the retina could be carried over to the colliculus and provide mapping/...