Spatial transcriptomics is dazzling but complex. Visium and Xenium map the landscape, and Via Foundry helps you navigate it.

Imagine landing in Tokyo in the 1980s. Neon lights, endless train lines, and hidden alleys stretch in every direction. Every corner promises something new. You unfold a paper map, circle your destination, maybe carry a compass and a stack of guidebooks. With enough patience, you’ll get there, but not without wrong turns, backtracking, and a constant sense of disorientation.

Fast forward to today: Tokyo fits in your palm. With QZSS-supported GPS and Street View, navigating a dense, intricate city feels effortless. You can zoom from a subway map down to the entrance of a ramen shop, and never get lost.

Spatial transcriptomics does the same for tissues. It reveals not just which genes are expressed, but also where, preserving the architecture of tissue in stunning detail. Xenium, Visium, and Visium HD generate extraordinary data, like the best printed maps and street-level photos.

But without a navigation system, researchers are left piecing it all together by hand. Manual annotations. Fragmented outputs. Endless technical detours.

Via Foundry changes all of that. It brings all three pipelines together in one place. Data becomes direction. Complexity gives way to clarity. Once you experience it, it’s hard to go back.

Spatial data is rich, but like Tokyo’s sprawl, hard to tame

Dr. Alper Kucukural, one of the founders of Via Foundry, lived this firsthand. “I was switching between Space Ranger, Seurat, and image alignment tools, trying to replicate published workflows but getting inconsistent results,” he recalls. “There was no single source of truth. Weeks passed and I was still stuck reprocessing the same samples.”

Stepping into spatial transcriptomics can feel like trying to master Tokyo’s rail system on your first day. The excitement is there, but the scale and complexity quickly hit.

The data itself is enormous. A single experiment can generate hundreds of gigabytes, far beyond what most lab computers can handle.

Annotations and metadata are fragile. Multi-sample slides demand careful labeling, and keeping track of which tissue belongs to which condition often becomes a tedious manual task prone to error.

Every platform speaks a different language. Visium, Visium HD, and Xenium each generate their own outputs, making cross-comparison an exercise in translation.

Batch effects blur the picture. When combining multiple slides or runs, technical noise creeps in, obscuring the biological signals researchers are actually looking for.

Without a unifying system, researchers end up spending their time debugging pipelines and juggling files instead of interpreting biology. It’s like trying to navigate Tokyo with three different maps, none drawn to the same scale, and no clear way to stitch them together.

The Update: Spatial Now Lives in Via Foundry

The maps are here, and now there’s a navigation system. Via Scientific has brought the full suite of 10x Genomics’ spatial technologies into Via Foundry. Alper’s earlier experience helped shape the platform.

• Visium and Visium HD give researchers tissue-scale and high-resolution maps of gene activity across samples.
• Xenium takes you down to the level of individual cells, showing gene expression in precise spatial context.

Together, these tools generate extraordinary data. Now, they can be explored, compared, and analyzed inside a single platform: Via Foundry.

Making spatial practical, powerful, and reproducible

With Visium, Visium HD, and Xenium now supported in Via Foundry, researchers can finally move through spatial analysis with speed and confidence. What once felt like endless manual detours becomes a streamlined path to results.

Removes friction

Massive spatial datasets no longer stall progress. Via Foundry scales effortlessly in the cloud, so experiments that generate hundreds of gigabytes can be processed without the bottlenecks of local computing. Runs that once took days can now finish in hours.

Builds confidence

Instead of juggling different outputs, every run produces standardized HTML reports and Seurat-ready objects. That means results are reproducible, consistent across experiments, and ready to share. Comparing outputs from Visium and Xenium no longer requires patchwork scripts or manual file conversions.

Adds flexibility

Spatial analysis is not one-size-fits-all. Via Foundry supports workflows from both Space Ranger and Xenium Ranger, and its modular design means you can attach different segmentation tools such as StarDist, test alternative annotation methods, and extend into downstream analysis. For Visium HD, researchers can customize bin sizes to balance resolution and coverage, and still keep results fully integrated with the rest of their workflow.

Future-proof

Via Foundry’s interactive Space Viewer lets you explore your tissue like a map: zooming, coloring by gene, and examining clusters in real time. Because the platform is modular, new quantification methods, visualization tools, or QC checks can be integrated as the field evolves without disrupting existing pipelines.

Researcher impact

For the scientist, this translates to clearer visuals to impress collaborators and reviewers, fewer hours lost to manual cleanup, and less risk of errors creeping in. More importantly, it means adopting spatial transcriptomics without needing HPC infrastructure or advanced coding skills.

A guided journey into spatial biology

Exploring a new city is most rewarding when you can wander freely, confident you won’t get lost. Spatial transcriptomics should feel the same. Visium, Visium HD, and Xenium reveal remarkable views of biology, from tissue neighborhoods down to single cells. But views alone are not enough. To make discoveries, researchers need to connect those views. To understand how the streets, alleys, and landmarks fit together.

That is what Via Foundry provides. It transforms spatial analysis from a maze of technical detours into a clear path. It guides researchers through massive datasets with speed and reliability. Instead of being slowed down by data wrangling, scientists can focus on the real questions and uncover answers faster.

Spatial biology is entering its most exciting chapter. With Via Foundry, you are no longer just holding the map. You are moving through the city with clarity, speed, and purpose.

For industry teams: Book a demo to see how your lab can accelerate spatial discovery.
For academics: Learn more about spatial pipelines through Foundry EDU and explore what’s possible.

Want a deeper dive into the technical challenges researchers face with spatial data? Check out our earlier piece: Spatial Transcriptomics at Scale: How to Overcome the Top 5 Data Hurdles.