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To track the positions of many cells and their molecular features, scientists once needed a collection of equipment, a broad range of skills, and time—lots of time. Those requirements kept many scientists out of spatial biology, until there was an easier way to do it.

Simone Codeluppi, PhD
Simone Codeluppi, PhD
Principal Scientist, Bioinformatics, Rebus Biosystems

In the past, spatial biology required quite a setup. “You need a microscope, an imaging chamber where you run your reaction, and quite a bit of patience because image acquisition requires quite a bit of time,” explains Simone Codeluppi, PhD, principal scientist, bioinformatics at Rebus Biosystems in Santa Clara, CA. “Then, you end up getting a ton of data to process, which requires additional knowledge and computational power.”

Instead, an integrated system could dramatically simplify spatial biology. “It’s great to have an automated instrument that runs everything from sample handling to data processing,” said Codeluppi. That’s what a scientist gets with the Rebus Esper, which provides high-resolution imaging data that includes single-cell analysis and spatial mapping.

Rather than putting together a system and figuring out how to collect and analyze the data, a scientist can put in less than an hour of hands-on time to prepare a sample, put it in a flow cell, load and run the Rebus Esper, and collect the data. The results include a cell-by-feature matrix that can be loaded in a scientist’s preferred software to precisely map the cells and analyze them one by one. In less than two days, a scientist can collect tens of millions of data points on hundreds of thousands of cells.

Combining capabilities

In many cases, it takes a team of scientists to run a spatial biology type of experiment. When Codeluppi worked in a lab, he said, “I would focus on one part of the experiments, like the analysis, and then another colleague would set up the reaction and the imaging. Traditional technology usually required the development of such a team of scientists. “We split the work,” Codeluppi noted. “Otherwise, it was impossible for one person to run it.”

The combination of technologies in the Rebus Esper make it possible for one person to run complete experiments. Plus, this system sidesteps any complex learning curve. “You put the chamber into the machine and then you select the program to run,” Codeluppi states. A specific sample and research question, though, will probably require some adjustments. “No program is perfect,” Codeluppi pointed out. “So, you may need to run some tests, but you can do this optimization on the machine.”

Codeluppi and his colleagues keep adding options to the Rebus Esper. “We’re developing a solution that lets you run and analyze your data and be able to modify the parameters for the analysis by looking at intermediate steps,” he notes. “So, you can do some QC along the way.”

Instead of leaving a scientist swimming in a sea of options, the Rebus Esper keeps the adjustable parameters manageable. “There are certain parameters you can modify, but they are limited to those necessary for optimizing your experiment,” Codeluppi explaines. “This is another way we make it easier to use the Rebus Esper.”

In addition to combining capabilities, this platform also lets scientists focus on their questions. For example, a study can be run automatically, and the scientist can focus on the data. “You can decouple the data generation from the analysis,” as Codeluppi describes it. “So, you can really focus on the biology.”

Ultimately, a scientist seeks a spatial biology solution that can be used in a way that fits a lab’s workflow. That’s exactly what a scientist can do with the simplicity and flexibility of the Rebus Esper.

 

Learn more about the Rebus Esper.