The Power of Visualizing Tissue in 3D

Stellaromics Newsletter | July 2025

Tissue is not paper thin. It's time to stop studying it that way. In this month’s newsletter, explore how 3D spatial biology is powering advances in preclinical and translational research that 2D spatial cannot capture - with a focus on studies from neuroscience and metabolism research. We also highlight several analysis methods for 3D spatial transcriptomics, including the alpha release of our platform, PyxaStudio™!

Featured Research: Spatial transcriptomics AI agent charts hPSC-pancreas maturation in vivo

In a recent publication from Harvard and Penn, STARmap – the flagship technology behind Pyxa™ – was refined to analyze pancreatic xenografts using STAgent, a new AI agent designed to streamline the analysis of spatial transcriptomics data.
Learn how the 3D analysis of pancreatic tissue powers diabetes R&D, and how STAgent accelerates spatial transcriptomics data analysis down to minutes.

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Lin Z, Wang W, Marin-Llobet A, Li Q, Pollock SD, Sui X, Aljovic A, Lee J, Baek J, Liang N, Zhang X, Wang CK, Huang J, Liu M, Gao Z, Sheng H, Du J, Lee SJ, Wang B, He Y, Ding J, Wang X, Alvarez-Dominguez JR, Liu J. Spatial transcriptomics AI agent charts hPSC-pancreas maturation in vivo. bioRxiv [Preprint]. 2025 Apr 4:2025.04.01.646731. doi: 10.1101/2025.04.01.646731. PMID: 40236029; PMCID: PMC11996516. Distributed under CC BY 4.0.

See your sample in 3D: Get to know PyxaStudio™

When you purchase a Pyxa or partner with us for a services project, your data can be seamlessly explored in PyxaStudio, our dedicated visualization tool for navigating 3D gene expression maps, annotating spatial patterns, and quantifying transcript localization in volumetric context.

We’re excited to announce that PyxaStudio made its way into customers’ hands for the first time this month! This marks an exciting milestone in empowering scientists to explore 3D data and derive novel insights in neuroscience and beyond.

Hear from our customers: The impact of 3D on neuroscience research

“A key advantage of Pyxa over other spatial transcriptomic technologies is its ability to analyze much larger tissue volumes per experiment. By enabling dense reconstructions of intact neural circuits in 3D, Pyxa will significantly advance neuroscience research, particularly for our laboratory's goal of reconstructing cell type-specific synaptic connectivity relationships in high-throughput by tracking the synaptic spread of viruses using RNA barcoding.”

- Arpy Saunders, Assistant Professor at the Vollum Institute of OHSU