Lyα tomography surveys have begun to produce 3D maps of the intergalactic medium opacity at z ∼ 2.5 with megaparsec resolution. These surveys provide an exciting new way to discover and characterize high-redshift overdensities, including the progenitors of today’s massive groups and clusters of galaxies, known as protogroups and protoclusters. We use the IllustrisTNG-300 hydrodynamical simulation to build mock maps that realistically mimic those observed in the Lyα Tomographic IMACS Survey. We introduce a novel method for delineating the boundaries of structures detected in 3D Lyα flux maps by applying the watershed algorithm. We provide estimators for the dark matter masses of these structures (at z ∼ 2.5), their descendant halo masses at z = 0, and the corresponding uncertainties. We also investigate the completeness of this method for the detection of protogroups and protoclusters. Compared to earlier work, we apply and characterize our method over a wider mass range that extends to massive protogroups. We also assess the widely used fluctuating Gunn–Peterson approximation applied to dark-matter-only simulations; we conclude that while it is adequate for estimating the Lyα absorption signal from moderate-to-massive protoclusters (≳1014.2 h −1 M ⊙), it artificially merges a minority of lower-mass structures with more massive neighbors. Our methods will be applied to current and future Lyα tomography surveys to create catalogs of overdensities and study environment-dependent galactic evolution in the Cosmic Noon era.

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