This article has been updated to note that 10x Genomics plans to launch a new version of Gem-X Flex that has a plate-based workflow.
NEW YORK – The Advances in Genome Biology and Technology (AGBT) general meeting is not just about sequencing ─ in recent years, single-cell and spatial omics firms have also flocked to sunny Florida to showcase their technologies.
This year was no exception: companies including Bruker, Illumina, 10x Genomics, Singular Genomics, Scale Biosciences, and Parse Biosciences touted better multiplexing, throughput, and multiomics capabilities for their technologies at AGBT last week. Element Biosciences, meanwhile, provided an update on its Aviti24 multiomic platform ─ including in situ RNA sequencing ─ ahead of the conference.
Bruker
In its first AGBT meeting since acquiring NanoString Technologies last May, Bruker highlighted a suite of four platforms — CosMx Spatial Molecular Imager, GeoMx Digital Spatial Profiler, PaintScape, and CellScape — which the company hopes can cater to the different needs of spatial biology customers.
"The key takeaway is that each of the platforms does what they do best," Mark Munch, president of Bruker Nano Group, told GenomeWeb. "Each platform was designed to serve a different set of unique research needs in different application areas."
For CosMx, developed by NanoString, the company emphasized its whole transcriptome capability, which promises to capture 18,933 RNA targets with subcellular resolution, and its compatibility with formalin-fixed, paraffin-embedded (FFPE) samples. Along with RNA, CosMx can now detect up to 75 protein targets with single-cell resolution, using the same slide as the whole-transcriptome imaging, according to Joe Beechem, CSO and senior VP of R&D at Bruker Spatial Biology.
During a conference presentation, Beechem showed company-generated whole-transcriptome data for CosMx, now available as a preprint on BioRxiv. He and his colleagues analyzed six different human FFPE tissue types ─ colon, pancreas, hippocampus, skin, breast, and kidney ─ and were able to generate 5.4 billion transcripts from 2.7 million cells. The experiment yielded more than 1,550 transcripts and 900 unique genes per cell, on average.
For GeoMx, Bruker has expanded its protein panel to 1,000 targets, enabling the platform to perform spatially resolved protein and whole-transcriptome analysis simultaneously on the same sample. Bruker said the 1K protein panel for GeoMx is expected to start shipping this summer.
On the eve of AGBT, Bruker also launched PaintScape, a new platform that promises to achieve direct in situ visualization of the 3D genome in individual cells by leveraging the JebFISH technology.
According to a company presentation at AGBT, JebFISH, which is currently compatible with cell line and fresh-frozen tissue samples, uses a proprietary multiplexed barcode chemistry to define and identify loci. Munch said PaintScape will be on the market this summer.
Lastly, Bruker announced enhancements to its CellScape platform for spatial proteomics. With a new software engine called PowerOmx, CellScape now promises "improved throughput, image processing, and data integrity." According to the company, CellScape instruments with PowerOmx are shipping immediately, and customers with existing instruments will be eligible for upgrades.
Commenting on Bruker Spatial Biology's business roadmap post the Nanostring acquisition, Munch said the company prefers to keep Nanostring's "innovativeness, entrepreneurs, and their identity."
"We are not massive consolidators," Munch said. "We leave what makes companies special and try to make the infrastructure available."
Todd Garland, president of Bruker Spatial Biology, addressed the legacy legal proceedings against NanoString and said the company can now "sell every box, everywhere in the world."
Illumina
Heading into the single-cell and spatial omics market with full steam, Illumina offered updates on its sprawling multiomics product line at AGBT.
According to Cande Rogert, the company's VP and global head of advanced sciences, Illumina's single-cell sample prep product, obtained through the Fluent BioSciences acquisition last year, is on the market. The company also plans to launch its proteomics assay, called Illumina Protein Prep, during the first half of the year and a single-cell Perturb-seq product in the second half. The five-letter seq epigenetic analysis assay is slated to come out in the first half of 2026.
In addition, Illumina highlighted its Connected Multiomics software, which is currently in early access. According to Rogert, the software can analyze transcript data based on automated cell segmentation, with visual spatial data overlaid on H&E-stained tissue images, and perform additional tertiary analysis such as differential expression, marker gene identification, and cell typing.
During an Illumina-sponsored workshop at AGBT, early-access customers for the company's recently unveiled spatial technology showcased their data and shared their experience. "The scale of data we can generate with this platform is really incredible," said Nicholas Banovich, a researcher and spatial biology expert at the Translational Genomics Research Institute (TGen).
Banovich's team employed the Illumina spatial technology to characterize alveolar dysregulation in pulmonary fibrosis. They analyzed eight flash-frozen lung tissue samples — including two controls and six disease samples — across two spatial slides, generating data for more than one million cells.
Overall, Banovich said he is "really impressed" with the high sensitivity of the assay and its ability to "recover many counts" for every detected gene within a cell. "Even for pretty low-quality samples, we are still getting quite a reasonable number of genes detected in these data," he added.
"Even with not-ideal samples, we captured a lot of features," agreed Jasmine Plummer, director of the Center for Spatial Omics at St. Jude's Children's Research Hospital, another early-access customer for the Illumina spatial technology.
Plummer's team used the Illumina spatial assay to study prostate cancer samples. Overall, she said the technology was able to generate "consistent representation of the spatial features across all samples regardless of the tissue size or the coverage." In her experiment, Plummer was able to obtain more than 60,000 RNA features in roughly four million cells. She also applauded the technology's large capture area, which allowed her team to "start digging more and more into the data in a meaningful way.
Similarly, Michal Lipinski, a senior research scientist with the Broad Institute's spatial technology platform, another early-access customer, said the large area of Illumina's spatial technology and its subcellular resolution are "great" for discovery-oriented profiling of large tissue areas, including the reconstruction of organs.
Lipinski's group analyzed mouse brain development using the Illumina spatial technology. They sectioned mouse forebrain samples and placed 10 sections on one Illumina spatial slide.
Overall, Lipinski said the method enabled them to profile 900 to 1,500 unique transcripts per cell, corresponding to 600 to 900 genes, with "very little" batch effects between the sections and across the slides.
Illumina's Rogert explained the inner workings of the Illumina spatial technology in more detail in an interview. The technology involves a barcoded substrate with 1 μm continuous features that capture poly-A RNA transcripts. Afterward, cDNAs are generated for the captured RNA, followed by RNA-seq library preparation and sequencing. After sequencing, the DRAGEN software combines the sequencing reads and the H&E staining image of the substrate to regenerate the transcriptome profile of the tissue sample.
This workflow appears to be similar to that of Stereo-seq, developed by researchers from China's BGI Group.
Currently, the Illumina spatial technology is not compatible with FFPE samples but Rogert said that is "100 percent in our roadmap, with other analytes and automation as well."
According to Joel Fellis, Illumina's VP of product management, the company plans to launch the spatial technology commercially in the first half of 2026 and is partnering with the Broad Institute to provide it as a service later this year.
Fellis declined to provide pricing information but said that the technology will be "at least four times less expensive per unit area versus the other alternatives out on the market."
10x Genomics
At AGBT, 10x Genomics discussed the roadmap for its single-cell and spatial products, noting that new product announced at the meeting will be available later this year.
10x Chief Technology Officer and founding scientist Michael Schnall-Levin said in an interview that the company is expanding its multiomics capabilities, streamlining its workflows, and boosting the scalability of its technologies.
For single-cell analysis, he highlighted an upcoming extension of the Chromium Gem-X Flex product line, a plate-based version that promises to expand the number of samples per run. At launch, this new version of Gem-X Flex will be able to accommodate more than 700 samples per run. Researchers will be able to use the new plate-based workflow to recover approximately one million cells from a single lane and eight million cells per chip.
In addition, the new Gem-X Flex version does not require users to fill an entire plate at once. Researchers will also be able to partition millions of cells in minutes using Chromium X and iX instruments as part of this plate-based workflow, according to the company.
For spatial biology, 10x announced several feature additions to the Visium HD platform at AGBT. For one, the company will be launching the Visium HD 3' assay, a reverse transcription-based product for whole-transcriptome spatial profiling at the single-cell level.
The company further released Visium HD Cell Segmentation, which leverages H&E staining images and the CytAssist software to achieve morphology-guided spatial transcriptomics analysis at the single-cell level.
Lastly, 10x highlighted Visium HD XL, which promises to capture an expanded area to enable whole-transcriptome spatial analysis of larger tissue sections at the single-cell level.
For the Xenium platform, the company is going to launch an RNA+Protein Multiomics product that can simultaneously measure RNA and protein targets on the same tissue slide. According to Schnall-Levin, the Xenium RNA+Protein assay will initially enable human 28-plex protein and 500-plex RNA analysis. The assay will be FFPE-compatible and commercially available by the middle of this year.
Last month, the Chan Zuckerberg Initiative launched the Billion Cells Project in collaboration with 10x and Ultima Genomics to create a dataset to train AI models in biology. Schnall-Levin said he sees a trend of increasing large single-cell and spatial projects as scalable technologies continue to become accessible.
"We are seeing quite a few academic groups, as well as biotechs, that are interested in doing large-scale studies," Schnall-Levin said. "I think as the technology continues to scale and gets less expensive, and as people have started learning how to really work with the data, and other ancillary tools have come together, the demand is really starting to come together for much larger-scale projects."
Singular Genomics
Singular Genomics Systems arrived at AGBT a few days after going private, as it was acquired by Deerfield Management Company in a deal that closed Feb. 19.
At the conference, Singular presented updates on its G4X Spatial Sequencer, which combines next-gen sequencing with FFPE tissue-based transcriptomics, proteomics, and fluorescent H&E imaging in a single system. The platform is currently in early-access testing by researchers at Beth Israel Deaconess Medical Center and at Vanderbilt University Medical Center. Singular plans to expand its early-access program to more sites in the second quarter.
The company is taking pre-orders for the G4X now and plans to ship the first commercial units in June. Meanwhile, it is offering services to researchers wanting to generate multiomics data on the platform.
According to marketing materials, the G4X can image up to 40 samples, each 10 mm x 10 mm in size, across four flow cells per run with 0.5 μm resolution, or up to 128 smaller samples, covering 30 million to 40 million cells in total.
Singular offers panels of up to 350 genes and 12 proteins for spatial analyses. Among them are a core immune panel as well as breast, lung, colon, and kidney panels, to which customers can add up to 25 genes of their choice.
Internally, the company has also used the system to reconstruct a tissue in 3D, using 10 serial sections from a renal cell carcinoma FFPE sample on a single flow cell that covered more than 6.2 million cells and 438 million transcripts.
In addition, it has internally demoed Direct-Seq, an in situ RNA sequencing method that enables sequencing of variable regions in antibodies and T-cell receptors directly in tissues, showing data from peripheral blood mononuclear cells (PMBCs) as well as from FFPE and fresh-frozen tonsil tissue at its conference suite.
Scale Biosciences
Single-cell analysis firm Scale Biosciences announced the availability its QuantumScale Single Cell RNA kits at AGBT last week.
Based on the company's quantum barcoding technology, the kits can capture between 84,000 and 4 million cells. According to Giovanna Prout, president and CEO of Scale Bio, "the magic happens" on the second of two plates, after reverse transcription. That second plate has 96 wells with microwells that contain a pool of barcoded beads. "So instead of 96 or 384 barcodes, we have 800,000 barcodes in that step, which gives us a 600-million barcode space," she said. "And this is really just the beginning of the barcode space that we can apply to this instrument-free plate-based workflow." Barcoding is followed by indexing and sequencing on either Illumina or Ultima platforms.
Cell recovery is between 60 percent and 70 percent, and the multiplet rate is less than 4 percent, which she claimed is the lowest rate in the market.
Using the company's ScalePlex technology, customers can multiplex up to 9,216 samples per run. "This is really ideal for population studies, for CRISPR and drug screens, for foundation model creation, where you can not only do 256 samples or 384 samples in a given workflow, but you can really tune the number of samples and cells all the way from eight samples or one sample to over 9,000 samples," Prout said during a company-sponsored workshop. As of now, Scale Bio uses 96 barcodes in 96 wells but it eventually wants to go up to 384 barcodes, she added.
The kits come in four configurations, depending on experiment size. Small kits go up to 85,000 cells, medium kits to 168,000 cells, and large kits to 2 million cells. The company's newest, extra-large kit goes up to 4 million cells, priced as low as 0.8 cents per cell. "No matter the scale that you're running … the workflow is extremely short, less than a day and a half for hands-on time and total time," Prout said.
As an example of a project using the 4 million cell kit, she mentioned a drug screen with more than 1,000 conditions and about 3,500 cells per condition. Such a screen would have a total cost of $54,600, with a per-sample cost of $47 and a per-cell cost of 1.3 cents, she said.
The company is already using the new kits as part of the 100 Million Cell Challenge, a collaboration between Scale Bio, Ultima Genomics, Nvidia, the Chan Zuckerberg Initiative, and BioTuring announced last year.
Prout said ScaleBio is working on extending QuantumScale to FFPE and other archival samples, starting with human, and on adding CRISPR enrichment. The company has a growing number of collaborators including spatial omics firms Vizgen and Takara's Curio Bioscience, "because single-cell and spatial are so complementary," she said.
Parse Biosciences
The week before AGBT, Parse Biosciences announced its single-cell RNA sequencing kits, called Evercode WT Penta and Penta 384, to analyze 5 million cells and 384 samples in a run. Both will start shipping to customers in mid-March. The company claims it is the only one that can profile gene expression of five million cells in a single run.
During a Parse-sponsored workshop at AGBT, Chief Technology Officer Charlie Roco said the firm is now working with more than 2,500 laboratories in 42 countries around the world, claiming it is "the fastest-growing single-cell company." Customers include labs at the New York Genome Center and Stanford University.
Roco called the firm's ability to detect genes and transcripts "unmatched" and stressed the low rates of doublets and ambient RNA. Similar to Scale Bio, no special instrumentation is required with Parse Bio. The workflow is based on cell fixation and is compatible with many types of commercially available sequencing platforms. Several rounds of plate-based barcoding allow for a total of more than 113 million barcodes, he said.
A comparison conducted by customers of Parse and 10x Genomics for single-cell RNA-seq demonstrated that Parse had a 20 percent higher gene detection rate and found more rare cell types in PBMC samples, Roco noted.
About a year ago, Parse acquired a data analysis company called Biomage, which Roco said has been "integrated phenomenally" with the company. "We can actually now start doing really, really in-depth analysis," he said.
Parse has also worked with several automation companies including Integra, Opentrons, Sptlabtech, and Hamilton. "We can get very intentional to make sure we have automation solutions for different types of researchers," he said.
Recently, Parse has "seen a big need to scale in a number of different areas," he said, such as high-throughput drug and target screening, building datasets to train AI models, and clinical trials and population studies. For such very high-throughput projects, Parse is offering an in-house service called GigaLab that can accommodate projects with more than 10 million cells and up to 1,152 samples. As an example, he showed a project with researchers in Munich to screen 90 cytokine treatments on 18 cell types from 12 donors. The barcode preparation step for this took three days, and sequencing on the Ultima Genomics platform another week, followed by about a week of data processing. "Altogether, it's basically 2.5 weeks here to do 10 million cells from start to finish," he said.
For another, even larger project in collaboration with Vevo, the Arc Institute, and Ultima Genomics, results from which were recently published as a preprint, Parse analyzed 50 tumor models treated with 400 drugs in three concentrations. This resulted in almost 62,000 samples, more than 101,000 cells, and 1.5 trillion sequencing reads, and took 19 days from cells to sequencing libraries. "This is an unprecedented experiment," Roco said. "This is going to change the way you can do biology experiments."