Standardization infrastructure for quantitative fluorescence microscopy

Cytely was founded in Lund, Sweden in 2021, in the research environment adjacent to Lund University and Skåne University Hospital. The observation was specific: fluorescence microscopy is among the most widely used quantitative tools in the life sciences, yet the intensity measurements it produces are systematically non-comparable across instruments — not because of biology, but because of physics. Detector gain, laser power calibration, filter transmission, and optical flatfield all vary between systems — and no established software infrastructure existed to correct for these differences in a protocol-driven, auditable way.

Philip Nordenfelt, Cytely's founder, arrived at this problem through cell biology research. Intensity measurements of DAPI-stained nuclei from the same slide, acquired on two confocal systems in the same core facility, differed by more than 30% in absolute value. The root causes — flatfield non-uniformity, detector gain offset, and per-session laser drift — were each individually understood. The absence was a standardized correction pipeline that a researcher could apply before analysis and document in a methods section.

Cytely addresses that gap. The platform operates at the image level, before any segmentation or quantification software runs — making measurements generated today, on one instrument, directly comparable to those generated next year, on a different instrument, in a different lab. This is not a new analysis method. It is standardization infrastructure that should have been part of every quantitative imaging workflow from the start.

Cytely is not a general-purpose image analysis suite. We do not replace CellProfiler, MATLAB-based pipelines, or vendor analysis software. We standardize the images before they reach those tools.