Deepcell Launches AI-Powered Single Cell Analysis Platform to Accelerate Cell Biology Discovery and Catalyze Field of Morpholomics

Benchtop REM-I Platform enables unprecedented insights into cell biology through scalable single cell imaging, high-dimensional analysis and cell sorting

Company to present research at CYTO 2023 highlighting deep learning capabilities of its artificial intelligence solution, the Human Foundation Model

MENLO PARK, Calif.–(BUSINESS WIRE)–#AIDeepcell, a pioneer in artificial intelligence (AI)-powered single cell analysis to fuel deep biological discoveries, today announced the launch of the REM-I Platform, a high-dimensional cell morphology analysis and sorting platform which comprises the REM-I benchtop instrument, Human Foundation Model, and Axon data suite. By bringing together single cell imaging, sorting, and high-dimensional analysis, the REM-I Platform will catalyze new methods of discovery in a wide range of fields including cancer biology, developmental biology, stem cell biology, gene therapy and functional screening, among others. Deepcell’s leaders will present data on the company’s AI-based morphology profiling solutions, which leverage the company’s proprietary deep learning and computer vision model, during three scientific podium presentations at CYTO 2023 in Montreal, Quebec, May 20-24, 2023.

“Deepcell’s approach to bringing artificial intelligence into cellular analysis will revolutionize biological research, ushering in a new era of discovery,” said Maddison Masaeli, PhD, cofounder and chief executive officer at Deepcell. “We empower our customers to rapidly transform biological research by applying the latest advances in AI to morphology, which is the bedrock of cell biology.”

Cell morphology was one of the first ways cells were studied since the advent of the microscope. Despite recent advancements in microscopy and flow cytometry, existing tools for cellular quantification and characterization have left the field of cell biology hypothesis bounded and reliant on human interpretation, until now. With the new generation of AI and machine learning models like Deepcell’s Human Foundation Model, cell morphology can finally join other high-dimensional, single cell analysis methods and enable researchers to realize the full potential of the morpholome.

“In the launch of the REM-I Platform we are witnessing the realization of years of first-principle thinking about the future of cell biology—a future liberated from the constraints of prior knowledge,” said Euan Ashley, MD, PhD, scientific cofounder of Deepcell, associate dean in the Stanford University School of Medicine and professor at Stanford University. “With the help of sophisticated artificial intelligence models, we can surpass the limits of what our eyes can see and peer ever more deeply into the biology of individual cells. I can’t wait to see what the scientific community does with this powerful new tool.”

REM-I Platform Enables Unbounded Single Cell Discovery and Analysis

Deepcell technology has been used to capture and characterize more than two billion images of single cells across a large variety of cell types. The Human Foundation Model, a self-supervised deep learning model trained on a subset of these unlabeled cellular images from a range of carefully selected biological samples, characterizes brightfield single cell images captured on the REM-I instrument and generates high-dimensional embedding data. Researchers can use the Axon data suite to access, visualize, and analyze these data in real-time and perform sorting of their cell groups of interest into up to six outlets on the REM-I instrument.

“Until now, the field of morphology has been limited to human interpretation of cellular features. Advancing morphology-powered discovery requires a new way of thinking to scale up and democratize single cell data generation and to enable unprecedented insights,” said Mahyar Salek, PhD, cofounder, president, and chief technology officer at Deepcell. “Advances in machine learning will transform our understanding of cell phenotype akin to the way next-generation sequencing transformed our understanding of the genome.”

Deepcell launched its Technology Access Program with the Translational Genomics Research Institute as well as University of California San Francisco, which leveraged the technology to study human cell lines, bodily fluids and solid tissues as part of cancer research and drug screening projects.

The company recently completed its first European installation of the Deepcell technology through its Technology Access Program at the Erasmus Medical Center in Rotterdam, which will use the instrument to study immune therapies from cancer patient samples.

“The Deepcell platform gives us the ability to discriminate between activated and naive T cells and provides next-level detection of therapy response in peripheral blood mononuclear cells derived from patients treated with immune therapies for cancer,” said Peter van der Spek, professor, Department of Pathology and Clinical Bioinformatics, Erasmus Medical Center. “Pathologists can increase the throughput of samples and assess many more cells than by conventional light microscopy.”

The REM-I Platform is available for orders and expected to begin shipping to customers in early 2024. For more information visit,

CYTO Presentations Validate Deepcell’s AI-Driven Approach to High-Dimensional Biology

Three scientific abstracts sharing data developed by Deepcell scientists were selected for scientific talks at CYTO 2023 from among hundreds of submissions. In addition to these presentations, the company will also reveal the REM-I instrument and demonstrate its capabilities at the conference.

Presentation Title: Deep learning models capture multi-dimensional features for cell morphology analysis from brightfield images

Time and Location: May 22 at 10:30 a.m. in room 512B

Presenter: Mahyar Salek, PhD, president, chief technology officer, and cofounder, Deepcell

Presentation Title: A novel platform using deep learning to perform label-free multi-dimensional morphology analysis for biological discoveries

Time and Location: May 24 at 10:30 a.m. in room 511E

Presenter: Maddison Masaeli, PhD, cofounder and chief executive officer, Deepcell

Presentation Title: Multi-omics analysis integrating deep learning morphology profiling and single cell RNA-seq reveals lung tumor heterogeneity and enriches tumor sub-populations

Time and Location: May 24 at 10:30 a.m. in room 512B

Presenter: Nicholas Banovich, PhD, chief scientist, Deepcell

For more information about the Deepcell’s activities at CYTO 2023, visit booth #238 or our CYTO 2023 Microsite.

About Deepcell

Deepcell is a life science company which brings artificial intelligence to cell biology, unlocking a new field of high-dimensional biological discovery known as morpholomics. Through Deepcell’s AI-powered imaging and microfluidics solution, the REM-I Platform, the company is enabling a new scale of cell biology research and single cell analysis leveraging cellular morphology for unbounded discovery. Deepcell’s platform leverages its artificial intelligence model, the Human Foundation Model, to identify and sort cells based on morphological distinctions helping power basic and translational research and offering future applications in diagnostic testing and therapeutics targeting. The company was spun out of Stanford University in 2017 and has raised nearly $100 million in venture capital. It is based in Menlo Park, California. Learn more at or follow us on Linkedin, Twitter, and YouTube.


Gwen Gordon

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