Exploring Cells & Systems via Image Analysis and Customized Microscopy
Previous and Current Research
We are best known for BLAST and the whole-genome shotgun protocol and assembler — accomplishments in traditional sequence-based bioinformatics. But since 2002 the group has focused almost exclusively on analyzing and extracting information from images obtained by various forms of microscopy. We believe that such data will reveal more about the function of the entities encoded in the genome then any other approach and will eventually become a prevailing paradigm of investigation, like sequence-based discovery is today. The group has even begun to develop its own customized microscopes.
Since 2002 we have worked on the following representative problems among others:
- Building a cell model of a C.elegans L1 larvae and software to automatically extract cell-by-cell expression levels in situ.
- Building models of the fly nervous system using light microscopy. By stochastically expressing GFP in every individual neuron in this brain, we expect to deliver a detailed view of the highly stereotyped neuronal connectivity of the fly brain.
- Tracking and measuring the vibrissae of a mouse while it is performing a cognitive function.
- Tracking microtubules and centrosomes during the first few cell divisions of the embryogenesis of C. elegans.
- Construction of an ultra-fast, block-face multi-photon microscope with onboard microtome for imaging a mouse brain with 1/2-micron pixels in less than a week.
In broad terms, the computational challenges are to build canonical 3D models of biological systems and map molecular observations onto the model. That is, there is the challenge of registering observations from different animals into a single representative framework, and the challenge of extracting meaningful information in the presence of low SNR and diffraction-limited resolution. The offsetting factor to low SNR and resolution is the presence of very strong prior knowledge about the morphology and dynamics of the entities under observation. Many of our new techniques thus involve what are called template-driven approaches.
We are in essence a technology group. Our aim is to develop microscopes and software that make observations of in situ and in vivo systems that enable our collaborative partners to advance molecular and cellular biology. We have worked closely with Stuart Kim (Stanford), Chris Doe (Oregon), Tony Hyman (MPI-CBG), Karel Svoboda, Gerry Rubin, Jim Truman, and Tzumin Lee (HHMI JFRC) as examples. The figure below illustrates imagery from three of our projects.
Future Projects and Goals
The overarching goal of our group is to build optical devices, collect molecular reagents, and develop analysis software to monitor in as much detail as possible the concentration and localization of proteins, transcripts, and other entities of interest within a developing cohort of cells for the purpose of working together with other groups in the Dresden area towards a biophysical understanding of development at the level of cell communication and force generation. Some of our projects are:
- Build a microscope for meso-scale observations that can image at 50fps or faster, with ~125nm isotropic resolution.
- Build a microscope for following the trajectory and expression of every nucleus of a developing fly embryo over a 24 hours period, with sufficient resolution to accurately track every cell but without “cooking” the embryo (i.e. < 30secs per stack, 3/4micron resolution 100 microns into the embryo, etc.)
- Track and build a model of every cell shape during fly wing or fly epitheliumdevelopment.
- Image all transcription factors in every cell, and every larval stage of C.Elegans and C.Briggsae.
- Understand transcription onset and the mechanism of Dauer exit.
- Build a long read-only assembler and use it to de novo reconstruct many interesting, large genomes.
Methodological and Technical Expertise
- NGS sequencing and assembly
- High throughput microscopy
- Image analysis / interpretation of microscope data sets
- Customized control systems for microscopy
- Algorithms and efficient use of computer hardware
N.G. Clack, D.H. O'Connor, D. Huber, L. Petreanu, A. Hires, S. Peron, K. Svoboda, E.W. Myers
Automated Tracking of Whiskers in Videos of Head-Fixed Rodents
PLoS Computational Biology 8 (2012)
M. Decker, S. Jaensch, A. Pozniakovsky, A. Zinke, K.F. O'Connell, W. Zachariae, E. Myers, and A.A. Hyman
Limiting amounts of centrosome material set centrosome size in C.elegans embryos
Current Biology 21, 15 (2011), 1259–1267
F. Long, H. Peng, X. Liu, S.K. Kim, and E. Myers
A 3D Digital Atlas of C. elegans and its application to single-cell analysis
Nature Methods 6, 9 (2009), 667–672
H. Peng, F. Long, and G. Myers
Automatic 3D Neuron Tracing Using All-Paths Pruning
Conf. on Intelligent Systems for Molecular Biology (Vienna, 2011), 239–247
E.W. Myers, G.G. Sutton, A.L. Delcher, I.M Dew, D.P. Fasulo, M.J. Flannigan, S.A. Kravitz, C.M Mobarry, K.H. Reinert, K.A. Remington, E.L. Anson, R.A. Bolanos, H.H. Chou, C.M. Jordan, A.L. Halpern, S. Lonardi, E.M. Beasley, R.C. Brandon, L. Chen, P.J. Dunn, Z. Lai, Y. Lian, D.R. Nusskern, M. Zhan, Q. Zhang, X. Zheng, G.M. Rubin, M.D. Adams, and J.C. Venter
A Whole-Genome Assembly of Drosophila
Science 287 (2000), 2196–2204