A new, detailed view of embryos growing cell by cell has been made possible by using fluorescent microscopy and a new computational framework. With this new system, cell nuclei can be tracked with high accuracy and speed. Cell lineage reconstruction is possible that allows observing embryos growing cell by cell.
The study was published in the journal Nature Methods. The scientists that developed this new methodology are from the Howard Hughes Medical Institute, Janelia Farm Research Campus in Ashburn, Virginia and also the Max Planck Institute of Molecular Cell biology and Genetics in Dresden, Germany. Fernando Amat and Philipp J. Keller were the lead scientists on the project.
A goal in developmental biology is to be able to reconstruct cell lineages in developing organisms. Achieving this goal would mean that the developmental process of a complex multicellular organism would be understood on a cell level. In this study, the new computational framework and fluorescent microscopy was used to perform the first cell lineage reconstruction of Drosophila melanogaster (fruit flies) nervous system development within the development of an entire embryo. Understanding and being able to track the development of the nervous system is of particular importance and has been a goal of scientists for a long time.
Whereas high powered microscopes have allowed observation of cells dividing in early embryonic stages, this new method allows the tracing back of cells to their origins in earlier embryonic stages. A researchers can chose a cell at any stage of development and trace its lineage backwards or identify its trajectory forward during the growth of an embryo. This is done by traversing through the massive amount of data that was obtained with fluorescence microscopy and then stored in a computer. The authors pointed out that the software program is efficient enough to run on a desktop computer with use of a graphics card.
The problem that was difficult to overcome in this type of study was to be able to follow individual cells on a large scale over a long period of time. The volume of data is tremendous and also the data is very complex. Cells in embryos have different shapes, can be densely packed and have different behaviors, which makes it difficult to identify and track particular cells. Image quality is also an important feature of the methodology that needs to be at a very high level. The computer system works by grouping shapes together to spot cells. The speed of the microscopy allows images to be captured quickly enough so that the cells cannot migrate away too fast before they are then captured in another image.
Four-dimensional, terabyte-size (a terabyte is a thousand gigabytes) data sets were constructed of embryonic development in three different organisms. The three organisms were fruit flies, zebrafishes and mice. Advanced stages of embryonic development were analyzed including up to 20,000 cells per time point. The speed was 26,000 cells min-1 at a single computer workstation. Only two parameters needed adjustment during the process and visualization and editing tools were available for efficient data curation.
As this methodology matures and after many types of organisms are studied, it may be a useful method for understanding some human diseases that have been attributed to errors in the developmental process. It may be that the error in development of a given physiological system could be pinpointed by the computerized ability to view embryos growing cell by cell.
By Margaret Lutze