Pathology labs now produce more image data than ever, from standard H&E slides to multiplex imaging and spatial biology. Moving that data between scanners, storage and analysis tools is often harder than it should be. In this Spotlight On, we look at cytario, a German digital pathology software company our team will be seeing at Biomarkers, CDx & Precision Medicine Europe in Basel on 13 to 14 October.
cytario is working on a specific problem: how do you connect pathology images, analysis tools and storage without tying researchers to one supplier?
Why digital pathology data gets stuck
Pathology has moved well past scanning slides. Labs now work with multiplex imaging, spatial biology and AI analysis, and each step creates larger, more complex files.
The systems holding that data haven't always kept up. Working in the field, the cytario team kept running into the same issues:
Large datasets still being shipped on physical hard drives.
Complicated pipelines just to convert images between formats.
Different systems applying the same standards in different ways.
Spatial biology tools that don't work well with each other.
Data and algorithms locked inside one supplier's software.
Researchers increasingly need to combine scanners, image management, algorithms and analysis tools from different providers. cytario's view is that another closed system won't fix this. An open base that lets those tools work together will.
From consultancy to software company
cytario is based in Harth-Pöllnitz in Thuringia, Germany, and works across digital pathology, spatial biology and computational pathology. The business grew out of Slash-m GmbH, a consultancy building custom medical software and pathology tools. After years of client projects, the team kept seeing the same gaps: tools that didn't connect, painful image conversions and data trapped in closed systems. cytario started as a side project to deal with those problems. In 2026, the team committed to it fully and turned the business into a dedicated digital pathology software company. The aim is an open base that lets pathology data, software and algorithms work together, rather than one more slide viewer.
What sets cytario apart?
Open source. The core software, cytario-web, is published on GitHub and npm under the AGPL-3.0 licence. Organisations can inspect it, host it themselves and adapt it. cytario's position is that reproducible science needs software people can check.
A team that knows the work. The team brings together histopathology, image analysis, spatial biology, AI, data science, software engineering and cloud infrastructure. They understand what a pathologist or spatial biologist needs, and what it takes to process that data at scale.
Standards you can check. cytario supports open formats including OME-TIFF and OME-NGFF/Zarr, with plugins for other formats. Two systems can claim the same standard and still not work together. Because cytario's code is open, its implementation can be tested and extended by anyone.
Customers keep their data. Organisations connect their own S3-compatible storage, whether in the cloud, on site or a mix of both. Their pathology data stays where they choose to keep it.
Designed for multiplex imaging from the start. Many image systems were built for brightfield pathology and adapted for fluorescence later. cytario was designed around multiplex immunofluorescence (mIF), with full 16-bit support and histograms, browser overlays for millions of cells, and storage built for very large image sets.
The platform: two layers on the same open standards:
Data Platform
The Data Platform is for viewing, sharing and organising whole-slide images at scale. It connects image viewing directly to the customer's own storage.
Image viewing for H&E, IHC and multiplex immunofluorescence.
mIF tools including split-screen viewing, channel controls, histograms and intensity readouts.
Analysis overlays that show segmentation, phenotyping and other cell-level results on top of the original tissue image.
Bring your own storage, reading directly from S3-compatible storage on site, in the cloud or both.
Open formats, so data isn't tied to one supplier.
Research Platform
The Research Platform adds image analysis to the same environment. Researchers can set up and run analysis pipelines inside the image management system, instead of exporting images to separate software.
That keeps the image, the analysis and the results in one place. Organisations can also plug in their own infrastructure, algorithms and tools.
Professional Services
Alongside the software, cytario offers project work built around the same workflows. Each project can draw on specialists in pathology, spatial biology, image analysis, AI, data science, software and cloud infrastructure, rather than one person.
Image analysis for mIF and H&E, including segmentation, phenotyping and spatial readouts.
AI model development, fine-tuning or building custom models on the customer's own data.
Data analysis covering spatial and single-cell work, clustering, integration and publication-ready results.
Infrastructure and scale, helping teams set up systems that can handle large pathology and spatial datasets.
Customers can hand cytario a whole project, or work alongside the team and keep running the workflows themselves afterwards. In each case, the starting point is the scientific question, which the team then turns into a workflow that can grow with the data.
Why it matters for pathology and spatial biology
As pathology and spatial biology rely more on computing, producing better data is only half the job. Labs also need the software and infrastructure to use it.
Researchers want tools that can handle larger datasets without tying them to one supplier. They also need people who understand both the biology and the practical side of working at scale. cytario is trying to offer both: open software, built and supported by people who know the workflows.
What it means for hiring
Companies in computational pathology need leaders who can work across science, software and infrastructure. Those profiles are rare, and both tools companies and pharma need them. Senior roles in this space include:
Heads of computational pathology and spatial biology who can set scientific direction and lead mixed technical teams.
Chief technology and product leaders who understand open-source models, data standards and cloud infrastructure.
Commercial leaders who can sell platforms and services into pharma, biotech and academic research.
Founders and CEOs moving from a consultancy model to a product company.
cytario's own recent hire of an experienced Head of Computational Pathology & Spatial Biology shows how much one senior appointment can add to a growing company.
What's next for cytario
cytario has launched self-sign-up access, so researchers can try the platform directly. It has also built a larger team of specialists to take on more complex projects.
Dr Lorenz Rognoni recently joined as Head of Computational Pathology & Spatial Biology. He brings 12 years of experience from Definiens, AstraZeneca, Ultivue and Vizgen.
The company's plans include:
Opening up access through the self-sign-up trial.
Adding more algorithm and computational integrations.
Supporting larger spatial and computational pathology projects, from routine lab work to high-dimensional and multi-omic tissue studies.
Meeting researchers and partners at Biomarkers, CDx & Precision Medicine Europe in Basel, 13 to 14 October.
"The bottleneck in spatial biology was never the science, it was the infrastructure: fragmented formats, shipped hard drives, and closed pipelines that locked data and algorithms inside a single vendor's ecosystem. We are building cytario so that infrastructure finally works in your favour." - Lorenz Rognoni, Head of Computational Pathology & Spatial Biology, cytario.
You can find out more and sign up for the trial at cytario.com.
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