This story has been updated to include products launched in 2024 from IonPath and Standard BioTools.
NEW YORK – Single-cell and spatial omics technologies have never been more powerful but selling them has never been harder than in 2024.
The past year saw single-cell sequencing methods break pricing barriers and spatial omics products push the envelope. However, competition in single-cell analysis is only getting more intense, and multiple companies focused on spatial technologies, including Akoya Biosciences, NanoString Technologies, and even 10x Genomics, experienced business-related headaches over the course of the year.
10x, active in both markets, has seen its shares fall more than 75 percent this year so far, while Akoya's share price has fallen 50 percent. NanoString was driven into bankruptcy in February and acquired by Bruker in April, and Vizgen restructured in March before merging with Ultivue in October. French single-cell startup Scipio Bioscience, meanwhile, announced in September that it was ceasing operations.
Despite these warnings, other companies have joined the fray. In February, sequencing startups Element Biosciences and Singular Genomics Systems announced new technology that would make their sequencers able to analyze single cells and do spatial multiomics, respectively. Soon after, Singular announced that it was shifting its focus from next-generation sequencing to sequencing-based spatial analysis. Meanwhile, Illumina, long content to support the back half of the single-cell sequencing workflow, acquired Fluent BioSciences and its single-cell isolation technology for approximately $85 million in July.
According to some, single-cell sequencing is seeing a boom. "Now is a great time for single-cell," Parse Biosciences CEO and Cofounder Alex Rosenberg said. "Researchers have more capabilities than ever, and new applications are coming online that no one would have even dreamed of a few years ago. We're seeing broader use cases … and more applications to translational research and clinical samples."
Moreover, researchers' projects are creating more demand. "[They're] asking more complex questions with single-cell that require more conditions, time points, treatments, and replicates," he said. Feeding artificial intelligence-based virtual cell models is one of those: Earlier this month, Parse announced the completion of a 100-million-cell dataset created in collaboration with Vevo Therapeutics for use in AI-based drug discovery. The data were created as part of Parse's GigaLab, a high-throughput single-cell sequencing service launched earlier this year.
"There has been a real step-change with customers planning super large-scale experiments — we're talking millions of cells or more," echoed 10x Cofounder and Chief Technology Officer Michael Schnall-Levin.
The drive toward bigger projects in single-cell sequencing may be aided by lower prices for high-throughput experiments. In February, 10x announced a new chip design for its single-cell gene expression assays called GEM-X, which it said could reduce costs per sample while improving sensitivity and cell recovery. Then, in October, the company announced a format for this product line that it claimed would reduce sample preparation costs to approximately $.01 per cell for runs of 2.5 million cells.
10x also launched an entry-level Chromium instrument, the Xo, which only runs the 3' gene expression assay and costs just $25,000.
Other single-cell sequencing companies also updated their product offerings this year. In addition to the GigaLab, Parse launched T-cell and B-cell receptor sequencing kits, a new chemistry, and a low-input fixation method, as well as its own data analysis platform, Trailmaker, acquired from Biomage. Scale Biosciences launched ScalePlex single-cell multiplexing technology and TotalSeq Phenocyte single-cell protein profiling in conjunction with Revvity's BioLegend. The firm also inked partnerships with Vizgen, SPT Labtech, Ultima Genomics, and Nvidia. Fluent, prior to its acquisition by Illumina, launched a new version of its chemistry in May.
In May, researchers from Carnegie Mellon University and the University of Washington introduced GAGE-seq, a single-cell assay that adds information on the 3D structure of the genome to gene expression data from the same cell.
Researchers looking to make sense of the different single-cell sequencing technologies on the market can turn to a benchmarking study from researchers at Genentech, which evaluated kits from 10 different companies. The study, posted as a preprint in June, emphasized new metrics such as cell recovery and sequencing efficiency, as well as standard ones like genes and unique molecular identifiers per cell. 10x's Gene Expression Flex kit stood out for its assay performance, though many of the startups noted that the study was not able to make use of improved products they had recently released or were going to launch soon.
Spatial awareness
Like single-cell technology providers, spatial biology companies struggled some in 2024, especially compared to 2023, which was a "nice revenue year" for spatial omics, according to Kyle Mikson, a diagnostics and life science tools company analyst at Canaccord Genuity. For example, 10x's third quarter spatial instrument revenues were approximately half of what they were in the prior-year period, though spatial consumables more than doubled, year over year, driven in part by the long-awaited launch of Visium HD earlier in 2024 and the Xenium Prime 5K panel. "The drop-off could be because markets are not quite ready to have tons of these boxes out there," he said.
Getting more boxes into the marketplace was also hard due to macroeconomic issues seen across the life science tools industry, with tighter budgets and careful spending. Single-cell and spatial omics companies were not alone, as even sequencing firms such as Illumina and Pacific Biosciences had difficulties. Over the first three quarters of 2024, Illumina's sequencing instrument revenues have fallen 37 percent compared to the prior-year period while PacBio's instrument revenues have declined 41 percent over the same interval.
Single-cell analysis and spatial omics product lines may even be competing with each other. "Single-cell and spatial have separate use cases, but to some extent they're targeting the same customers," said Subbu Nambi, an analyst at Guggenheim Securities. "They rely on a limited amount of research dollars."
Within spatial biology, the clinical and translational market is more developed than it is for single-cell sequencing. These customers "are not highly technical and want to get answers as quickly as possible," Nambi said, adding that they're willing to compromise on spatial resolution and multiplexing — 20 to 40 protein targets is the sweet spot — for flexibility in choosing those targets.
According to Nambi, Bio-Techne's Comet instrument, which the firm added to its portfolio in 2023 through its acquisition of Lunaphore, has "quickly become the go-to solution" for these customers. The product allows the use of any available off-the-shelf antibody, and slides can be later used for H&E staining.
In August, Minneapolis-based Bio-Techne said that demand for Comet was outpacing manufacturing capacity, and the firm reported in October that the product has helped drive diagnostics and spatial segment revenues to grow 14 percent in its fiscal first quarter 2025. Bio-Techne even renamed its "Diagnostics and Genomics" segment to "Diagnostics and Spatial" to reflect its shift in focus.
Comet's rise may have contributed to Akoya's dip, Nambi suggested, though Mikson noted that in addition to the macroeconomic environment, Akoya faced "various [additional] headwinds," including issues bringing manufacturing in-house and delayed biopharma partnerships in the first quarter. Akoya began the year with a license and distribution agreement with Thermo Fisher Scientific and ended it by signing a deal to develop and commercialize NeraCare's Immunoprint test for early-stage melanoma on the Akoya immunofluorescence platform. In between, the firm laid off about a third of its workforce but also announced that its PhenoCycler Fusion and PhenoImager HT platforms would be used as part of MANIFEST (Multiomic Analysis of Immunotherapy Features Evidencing Success and Toxicity) a UK-based effort to study immunotherapy in cancer.
Manufacturing its products in-house is allowing Akoya to "aggressively" launch new panels, CEO Brian McKelligon said, such as the PhenoCode Discovery IO60, an immuno-oncology panel, and the Mouse FFPE preclinical panel, both introduced in November.
IonPath and Standard BioTools also updated their spatial proteomics products this year. IonPath upgraded its MIBIscope platform to map cellular interactions at subcellular resolution while Standard BioTools added new modes for its Hyperion XTi platform.
New spatial omics methods also entered the fray this year. In October, researchers led by Holger Heyn of Spain's National Center for Genomic Analysis (CNAG), Jasmine Plummer of St. Jude Children's Research Hospital, and Luciano Martelotto of the University of Adelaide posted a preprint detailing a method using high-resolution spatial platforms, including NanoString's CosMx and 10x's Xenium, to analyze gene expression for large panels at single-cell resolution.
Called Single-Cell Transcriptomics Analysis and Multimodal Profiling (STAMP), the method lowers the cost per cell to approximately one half of a cent and does not require additional analysis by sequencing. The response since then has been "overwhelming," Martelotto said. "STAMP is reshaping the way many labs approach single-cell analysis. … In many ways, single-cell imaging is becoming the new single-cell sequencing."
What next?
Thirst for single-cell and spatial omics data should remain high. In November, the Human Cell Atlas consortium released dozens of papers built on such data, en route to producing a first draft sometime in 2026, with several more atlases coming out in the next several years.
"10 million is the new 1 million when it comes to cells profiled per project," Parse's Rosenberg said. "Everyone is scaling up across academia, biotech, and especially pharma. … We're very soon going to be seeing the first billion-cell datasets."
Meanwhile, Illumina said it would be rebranding Fluent as an Illumina product in early 2025 and expects "to accelerate the adoption of single-cell sequencing to the next wave of customers."
According to Akoya's McKelligon, researchers will be "using spatial transcriptomics coupled to spatial proteomics platforms on a more routine basis." Many spatial proteomics firms are already using single-cell sequencing as a complementary technology, he noted, and adding spatial transcriptomics is likely going to be next.
"We're excited for a world of practical multiomics, where all researchers have access to high-plex and high quality data that's able to be integrated with standards like H&E [staining]," 10x's Schnall-Levin noted.
But the ability to quench that thirst has been clouded by proposals to cut US government spending as President-elect Donald Trump prepares for a second term. "There are a lot of question marks about NIH funding and budget for the next four years," Mikson said.