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Fernando Amat

19700 Helix Drive

Ashburn, VA 20147

Phone: +1-571-209-4000

Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Google scholar profile: click here; Bitbucket repository: click here.

My name is Fernando Amat and I am a bioinformatics research specialist at HHMI Janelia Farm Research Campus. I work with Dr. Philipp Keller developing new statistical image processing and learning algorithms based on probabilistic models to tackle large-scale problems in biology. My main focus at Janelia is the in toto analysis of embryogenic development of complex organisms, such as zebrafish, Drosophila and mouse. Dr. Keller has developed state-of-the-art light-sheet based microscopes that allow to record the movement and division of every cell during embryogenesis for different organisms.


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 or behavioral biological questions. My goal is to develop new algorithms to process all this data efficiently and with minimum human interaction, in order to transform microscopy images into specific knowledge and to expand the set of scientific questions that can be answered.

I originally moved to Janelia Farm in 2010 to join Dr. Eugene Myers' lab as a postdoc. Before coming to Janelia Farm and the Washington DC area I graduated from another farm, Stanford University, in June 2010 in the Electrical Engineering department. My PhD advisor was professor Mark Horowitz and my co-advisor was professor Daphne Koller. My PhD thesis was "Image Alignment for cryo-Electron Tomography using Markov Random Fields".