Fernando Amat
I work with Dr. Eugene Myers and many other collaborators at Janelia applying statistical image processing and learning algorithms to tackle large-scale problems related to neuroscience. With the development of new imaging technologies and the adoption of digital systems for data acquisition, the amount of data collected in a single experiment can be in the realm of terabytes. Moreover, many experiments required long acquisition periods in order to capture all the necessary information to answer developmental biology questions. My goal is to develop new algorithms to process all this data efficiently and with minimum human interaction, in order to transform images into specific knowledge and to expand the set of scientific questions that can be answered. One example is our collaboration at Janelia with Dr. Keller's group to perform cell lineage reconstruction during the first 24 hours of development in zebra fish and flies. The goal is to track thousands of dividing cells at the same time with zero error in order to recover accurate cell lineages for each specimen.
Fernando Amat was was born in Barcelona, Spain. He graduated from Technical University of Catalonia (UPC) with a bachelor degree in Mathematics and another degree in Telecomunnication Engineering in 2004. He crossed the Atlantic Ocean to start his PhD in Electrical Engineering at Stanford University in September 2004. There he worked with Prof. Mark Horowitz and Prof. Daphne Koller in the area of bioimaging. In particular, he applied Markov Random Fields to image alignment problems in cryo-electron tomography. In 2010 he moved to the East coast in the Washington D.C. area to start a post-doc position in Gene Meyers’ group at Janelia Farm to keep working on bioimaging. In particular, neuroscience is a great field where computational tools and biology can benefit from each other. Moreover, Janelia is a rich multidisciplinary research environment where one can keep learning new things every day, which is what Fernando Amat is really interested on.
Janelia Publications
In the past few years, three-dimensional (3D) subtomogram alignment has become an important tool in cryo-electron tomography (CET). This technique allows one to produce higher resolution images of structures which can not be reconstructed using single-particle methods. Building on previous work, we present a new dissimilarity measure between subtomograms that works well for the noisy images that often occur in CET images. A technique that is more robust to noise provides the ability to analyze macromolecules in thicker samples such as whole cells or lower the defocus in thinner samples to push the first zero of the Contrast Transfer Function (CTF). Our method, Threshold Constrained Cross-Correlation (TCCC), uses statistics of the noise to automatically select only a small percentage of the Fourier coefficients to compute the cross-correlation, which has two main advantages: first, it reduces the influence of the noise by looking at only those peaks dominated by signal; and second, it avoids the missing wedge normalization problem since we consider the same number of coefficients for all possible pairs of subtomograms. We present results with synthetic and real data to compare our approach with other existing methods under different SNR and missing wedge conditions, and show that TCCC improves alignment results for datasets with SNR<0.1. We have made our source code freely available for the community.
Data acquisition of cryo-electron tomography (CET) samples described in previous chapters involves relatively imprecise mechanical motions: the tilt series has shifts, rotations, and several other distortions between projections. Alignment is the procedure of correcting for these effects in each image and requires the estimation of a projection model that describes how points from the sample in three-dimensions are projected to generate two-dimensional images. This estimation is enabled by finding corresponding common features between images. This chapter reviews several software packages that perform alignment and reconstruction tasks completely automatically (or with minimal user intervention) in two main scenarios: using gold fiducial markers as high contrast features or using relevant biological structures present in the image (marker-free). In particular, we emphasize the key decision points in the process that users should focus on in order to obtain high-resolution reconstructions.
Cryogenic electron tomography (cryo-ET) has gained increasing interest in recent years due to its ability to image whole cells and subcellular structures in 3D at nanometer resolution in their native environment. However, due to dose restrictions and the inability to acquire high tilt angle images, the reconstructed volumes are noisy and have missing information. Thus, features are unreliable, and precision extraction of the cell boundary is difficult, manual and time intensive. This paper presents an efficient recursive algorithm called BLASTED (Boundary Localization using Adaptive Shape and Texture Discovery) to automatically extract the cell boundary using a conditional random field (CRF) framework in which boundary points and shape are jointly inferred. The algorithm learns the texture of the boundary region progressively, and uses a global shape model and shape-dependent features to propose candidate boundary points on a slice of the membrane. It then updates the shape of that slice by accepting the appropriate candidate points using local spatial clustering, the global shape model, and trained boosted texture classifiers. The BLASTED algorithm segmented the cell membrane over an average of 93% of the length of the cell in 19 difficult cryo-ET datasets.
The surface layers (S layers) of those bacteria and archaea that elaborate these crystalline structures have been studied for 40 years. However, most structural analysis has been based on electron microscopy of negatively stained S-layer fragments separated from cells, which can introduce staining artifacts and allow rearrangement of structures prone to self-assemble. We present a quantitative analysis of the structure and organization of the S layer on intact growing cells of the Gram-negative bacterium Caulobacter crescentus using cryo-electron tomography (CET) and statistical image processing. Instead of the expected long-range order, we observed different regions with hexagonally organized subunits exhibiting short-range order and a broad distribution of periodicities. Also, areas of stacked double layers were found, and these increased in extent when the S-layer protein (RsaA) expression level was elevated by addition of multiple rsaA copies. Finally, we combined high-resolution amino acid residue-specific Nanogold labeling and subtomogram averaging of CET volumes to improve our understanding of the correlation between the linear protein sequence and the structure at the 2-nm level of resolution that is presently available. The results support the view that the U-shaped RsaA monomer predicted from negative-stain tomography proceeds from the N terminus at one vertex, corresponding to the axis of 3-fold symmetry, to the C terminus at the opposite vertex, which forms the prominent 6-fold symmetry axis. Such information will help future efforts to analyze subunit interactions and guide selection of internal sites for display of heterologous protein segments.
In the mouse, each class of olfactory receptor neurons expressing a given odorant receptor has convergent axonal projections to two specific glomeruli in the olfactory bulb, thereby creating an odour map. However, it is unclear how this map is represented in the olfactory cortex. Here we combine rabies-virus-dependent retrograde mono-trans-synaptic labelling with genetics to control the location, number and type of 'starter' cortical neurons, from which we trace their presynaptic neurons. We find that individual cortical neurons receive input from multiple mitral cells representing broadly distributed glomeruli. Different cortical areas represent the olfactory bulb input differently. For example, the cortical amygdala preferentially receives dorsal olfactory bulb input, whereas the piriform cortex samples the whole olfactory bulb without obvious bias. These differences probably reflect different functions of these cortical areas in mediating innate odour preference or associative memory. The trans-synaptic labelling method described here should be widely applicable to mapping connections throughout the mouse nervous system.
We present a method for automatic full-precision alignment of the images in a tomographic tilt series. Full-precision automatic alignment of cryo electron microscopy images has remained a difficult challenge to date, due to the limited electron dose and low image contrast. These facts lead to poor signal to noise ratio (SNR) in the images, which causes automatic feature trackers to generate errors, even with high contrast gold particles as fiducial features. To enable fully automatic alignment for full-precision reconstructions, we frame the problem probabilistically as finding the most likely particle tracks given a set of noisy images, using contextual information to make the solution more robust to the noise in each image. To solve this maximum likelihood problem, we use Markov Random Fields (MRF) to establish the correspondence of features in alignment and robust optimization for projection model estimation. The resulting algorithm, called Robust Alignment and Projection Estimation for Tomographic Reconstruction, or RAPTOR, has not needed any manual intervention for the difficult datasets we have tried, and has provided sub-pixel alignment that is as good as the manual approach by an expert user. We are able to automatically map complete and partial marker trajectories and thus obtain highly accurate image alignment. Our method has been applied to challenging cryo electron tomographic datasets with low SNR from intact bacterial cells, as well as several plastic section and X-ray datasets.