Part of the Oxford Instruments Group

New tools for tracing cell lineage and embryogenesis

New tools for tracing cell lineage and embryogenesis

Interest in studying embryogenesis — the formation and development of an embryo — greatly increased after the discovery that many of the genes at work during embryo development are turned back on when a tumor develops. One important aspect of studying embryogenesis is following the developmental history, or lineage, of all the embryo’s cells. The new Imaris 8.2 comes with tools that automatically trace cell lineages, providing both visual and quantitative cell lineage information that scientists can use to study how an organism creates a body plan and to learn more about the mechanisms involved in cancer.

Studying embryo development

Organisms such as C. elegansdrosophila, zebrafish and even chick and mouse embryos are used to study embryogenesis. Scientists want to understand how these organisms create a plan that directs cells to divide and signals daughter cells to become part of the heart, foot, or brain, for example. Teasing out this information requires tracing the fate of every single cell from the organism’s single-cell beginning throughout the process of embryogenesis.

Both embryo development and cancer involve high rates of cell division. Embryogenesis provides a useful model to test certain hypotheses about the function of certain genes and proteins during development, which in some cases also reveals their role in cancer. Scientists can also introduce genetic mutations or expose the embryo to a chemical, for example, and see how this affects development at a cellular level. These types of studies are typically conducted by expressing a transgene fused to a GFP molecule that fluoresces when excited by laser light.

Tracking thousands of dividing cells

Imaging and tracking lineages in living embryos over time comes with some challenges. With a living sample, you can’t turn up the laser power to get a stronger fluorescence signal because this will heat up the embryo causing it to become stressed, possibly to the point of dying. Software such as Imaris can greatly help by detecting each cell’s signal in an automated way, even when the signal-to-noise ratio is weak.


The next challenge is the fact that an embryo might contain millions of cells at any given time point. One of the first studies tracking cell lineage in an entire embryo involved the time-consuming task of manually following all the cells in the C. elegans embryo using differential interference contrast microscopy. This approach isn’t possible for larger embryos such as zebrafish or mice because they have far too many cells to follow manually and require fluorescence imaging approaches since DIC can’t image deep enough to see all the way through these embryos.  

Automatic cell lineage tracing

Imaris Lineage (from version 8.2) adds a variety of tools that overcome some of the challenges involved in tracking the lineage of cells in 3D. These new tools seamlessly integrate into the existing Imaris workflow and expand the ImarisTrack module for following objects in 3D.  

Imaris Lineage includes a new algorithm that detects cell division and automatically connects a mother cell with its two daughter cells, creating a lineage tree that depicts the genealogical relationships between cells as well as the time between cell divisions and cell generation. Each generation receives a corresponding color label in the tree and in the movie, so generations are easily visualized.

Even the best algorithm can miss a cell division due to image drift or a weak signal. New editing tools make it easer for users to visualize and manually edit any cell divisions that are missed by the algorithm. When the user clicks a particular cell on the automatically created lineage tree, the corresponding cell is highlighted in the movie. This lets the user examine that cell’s fate at the next time point and correct the branching in the lineage tree.

Quantitative data

Once the lineage tree is finalized Imaris can provide quantitative data on cell displacement, distance traveled, and speed of movement as well as the length of time that the cell was alive and the duration of the cell cycle. This information is important for gaining quantitative insights into cell movement and fate during development and understanding the effects of introduced gene mutations or other modifiers of signals involved in regulating cell fate.

Although Imaris can track the lineage of thousands of cells, sometimes just one cell or a small group of cells is of interest. A new Imaris feature (version 8.2 and later) makes it easier to visualize cells of interest by allowing the user to give specific cells a color and label. In the movie view, all the daughter cells that arise from that cell will also be labeled in the same color, allowing a researcher to determine how far specific daughter cells travel from their mother cells, for example.

With its Imaris Lineage package, Bitplane is meeting the needs of the increasing number of scientists who want to trace cell lineages and study embryogenesis. By automating cell lineage tracing and providing both visual and quantitative data, scientists can study embryogenesis and cell fate in more detail. The similarities between gene patterns found in developing embryos and tumors means that developmental biology research could lead to new and better treatments for cancer.

Category: Case Study

Download as pdf


Related assets