May 22, 2024

As a large contract research organization (CRO), CellCarta analyzes thousands of flow cytometry samples every month. CellCarta is leveraging automation tools such as CellEngine and laboratory information management systems (LIMS) for a seamless process. The deployment of CellEngine for clinical flow cytometry data analysis at CellCarta has significantly improved analysis quality and efficiency. CellEngine provides fast and scalable performance to handle large studies, automatic gating, and easy collaboration between analysts, principal scientists, and project sponsors. It provides an unmatched ability to deliver high-quality data in a timely manner.

In addition, CellEngine has a powerful application programming interface (API), enabling it to programmatically interact with other systems—for example, to automatically upload data from cytometers, integrate with bioinformatics pipelines, run custom algorithms, and create other highly specialized solutions. For example, CellCarta uses the API to automate parts of analysis and integration with CellCarta’s LIMS, enabling end-to-end integration and data management of studies:

  • After samples are acquired on a cytometer, they are automatically preprocessed to remove fluidic instabilities and other time-associated anomalies, then uploaded to the corresponding study in CellEngine. This removes any need to manually clean, move, and upload files, and makes data available almost immediately after acquisition.
  • Sample metadata is automatically pulled from the LIMS into CellEngine, allowing for immediate and accurate access to information such as the visit, patient ID, collection time, and any associated discrepancies. This ensures the availability of timely and accurate information alongside the data.
  • Automation continues to keep sample information up to date throughout the analysis. Whenever a change happens in the LIMS after acquisition, such as when a sample discrepancy is resolved, that change is automatically synced to CellEngine. This ensures that high-quality data is always available post-acquisition.
  • The use of CellEngine’s API further streamlines downstream processes, allowing for the data management, biostatistics and informatics teams to directly retrieve reportable (i.e., statistics) to prepare them for final reporting; eliminating slow and error-prone manual processing of data via exported spreadsheets.

Integration of these processes has led to a significant reduction in data analysis time, while increasing quality of data and enabling downstream data visualization capabilities.

“Integrating CellEngine with our LIMS system has transformed our data analysis workflow. By automating patient data input, we’ve boosted efficiency and accuracy, resulting in faster, higher-quality deliverables.”

– Alex Perieteanu, Vice President, Scientific Lab Operations, CellCarta

Interested in automating your analysis processes? CellEngine is available as a software as a service (SaaS), so you can benefit from the same features that CellCarta uses. Contact us for additional information, or start a free two-month trial at


About the author:

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Dariush Davani (PhD) is an immunologist with 20 years of clinical and discovery immunophenotyping experience. He is constantly fascinated by immune system’s mechanisms and powers in health and disease. At CellCarta his team analyzes a broad clinical trail flow and mass cytometry studies.