Figuring out how visual information travels from the retina to different parts of the brain requires understanding the many different kinds of cells involved, and since the retina is famously compact and complex, untangling the web of cell types and their roles in vision is a challenge for scientists.

One way to approach the cell types question is by using gene expression. Scientists often use specifically bred mouse lines, called Cre driver lines, which have precisely labeled markers that can be combined with a gene that makes only cells with a particular gene glow under the microscope.

Allen Institute for Brain Science researchers have been creating and describing Cre driver lines—and providing them to the community—for years, and have provided rich characterization of how those lines represent different cells in the brain. But until recently, the retina remained uncharted territory.

In work published together this week in the journal Cell Reports, Allen Institute for Brain Science and Harvard University researchers surveyed 88 Cre driver lines in the retina, uncovering the locations of cells expressing specific genes in the retina, and showing where those cells project into the brain.

“Our results reveal a rich variety of projection patterns from the eye to the brain,” says Julie Harris, Ph.D., Associate Director of Neuroanatomy at the Allen Institute for Brain Science. “This lends credibility to the idea that different kinds of cells in the retina play distinct roles in vision.”

Taking a widely used tool like Cre driver lines and applying it to the retina can help researchers understand not just the diversity of cell types in the retina, but also the usefulness and limitations of the tool itself.

“Cre is a helpful tool for identifying subsets of cells, but it’s not a direct translation of ‘cell type,’” says Harris. “Only a few Cre lines labelled just one kind of cell in the retina. More frequently, we saw several—often related—types labeled by one Cre line. Most likely, combinations of genes will be required to target specific cell types.”