  We present a new method of finding protoclusters using tomographic maps of
Ly$\alpha$ Forest flux. We review our method of creating tomographic flux maps
and discuss our new high performance implementation, which makes large
reconstructions computationally feasible. Using a large N-body simulation, we
illustrate how protoclusters create large-scale flux decrements, roughly 10
$h^{-1}$Mpc across, and how we can use this signal to find them in flux maps.
We test the performance of our protocluster finding method by running it on the
ideal, noiseless map and tomographic reconstructions from mock surveys, and
comparing to the halo catalog. Using the noiseless map, we find protocluster
candidates with about 90% purity, and recover about 75% of the protoclusters
that form massive clusters ($> 3 \times 10^{14} \, h^{-1} M_{\odot}$). We
construct mock surveys similar to the ongoing COSMOS Lyman-Alpha Mapping And
Tomography Observations (CLAMATO) survey. While the existing data has an
average sightline separation of 2.3 $h^{-1}$Mpc, we test separations of 2 - 6
$h^{-1}$Mpc to see what can be tolerated for our application. Using
reconstructed maps from small separation mock surveys, the protocluster
candidate purity and completeness are very close what was found in the
noiseless case. As the sightline separation increases, the purity and
completeness decrease, although they remain much higher than we initially
expected. We extended our test cases to mock surveys with an average separation
of 15 $h^{-1}$Mpc, meant to reproduce high source density areas of the BOSS
survey. We find that even with such a large sightline separation, the method
can still be used to find some of the largest protoclusters.
