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Abstract In multi-view fluorescence microscopy, each angular acquisition needs to be aligned with care to obtain an optimal volumetric reconstruction. Here, instead, we propose a neat protocol based on auto-correlation inversion, that leads directly to the formation of inherently aligned tomographies. Our method generates sharp reconstructions, with the same accuracy reachable after sub-pixel alignment but with improved point-spread-function. The procedure can be performed simultaneously with deconvolution further increasing the reconstruction resolution.