2 research outputs found
Toward single particle reconstruction without particle picking: Breaking the detection limit
Single-particle cryo-electron microscopy (cryo-EM) has recently joined X-ray
crystallography and NMR spectroscopy as a high-resolution structural method for
biological macromolecules. In a cryo-EM experiment, the microscope produces
images called micrographs. Projections of the molecule of interest are embedded
in the micrographs at unknown locations, and under unknown viewing directions.
Standard imaging techniques first locate these projections (detection) and then
reconstruct the 3-D structure from them. Unfortunately, high noise levels
hinder detection. When reliable detection is rendered impossible, the standard
techniques fail. This is a problem especially for small molecules, which can be
particularly hard to detect. In this paper, we propose a radically different
approach: we contend that the structure could, in principle, be reconstructed
directly from the micrographs, without intermediate detection. As a result,
even small molecules should be within reach for cryo-EM. To support this claim,
we setup a simplified mathematical model and demonstrate how our
autocorrelation analysis technique allows to go directly from the micrographs
to the sought signals. This involves only one pass over the micrographs, which
is desirable for large experiments. We show numerical results and discuss
challenges that lay ahead to turn this proof-of-concept into a competitive
alternative to state-of-the-art algorithms
Structural Variability from Noisy Tomographic Projections
In cryo-electron microscopy, the 3D electric potentials of an ensemble of
molecules are projected along arbitrary viewing directions to yield noisy 2D
images. The volume maps representing these potentials typically exhibit a great
deal of structural variability, which is described by their 3D covariance
matrix. Typically, this covariance matrix is approximately low-rank and can be
used to cluster the volumes or estimate the intrinsic geometry of the
conformation space. We formulate the estimation of this covariance matrix as a
linear inverse problem, yielding a consistent least-squares estimator. For
images of size -by- pixels, we propose an algorithm for calculating this
covariance estimator with computational complexity
, where the condition number
is empirically in the range --. Its efficiency relies on the
observation that the normal equations are equivalent to a deconvolution problem
in 6D. This is then solved by the conjugate gradient method with an appropriate
circulant preconditioner. The result is the first computationally efficient
algorithm for consistent estimation of 3D covariance from noisy projections. It
also compares favorably in runtime with respect to previously proposed
non-consistent estimators. Motivated by the recent success of eigenvalue
shrinkage procedures for high-dimensional covariance matrices, we introduce a
shrinkage procedure that improves accuracy at lower signal-to-noise ratios. We
evaluate our methods on simulated datasets and achieve classification results
comparable to state-of-the-art methods in shorter running time. We also present
results on clustering volumes in an experimental dataset, illustrating the
power of the proposed algorithm for practical determination of structural
variability.Comment: 52 pages, 11 figure