Microscopy automation projects on ZEISS ZEN
SmartLabs builds software that connects microscope control, image acquisition, analysis pipelines, external hardware, and reporting into one purpose-built workflow. Our projects help research and industrial teams automate imaging, measurement, inspection, and instrument-control tasks that the standard software does not fully support.
Case studies and project references
This project extends ZEISS Axioscan with a modular rare-event workflow. A preview scan is analysed using traditional image analysis or third-party AI to locate sparse targets, after which only those positions are acquired at high resolution. Operators can start from the full workflow, reuse an existing preview, or scan from previously defined ROIs, while new detection algorithms and models can be added without rebuilding the acquisition process.
We built a guided ZEN Blue extension for on-site sieve calibration and measurement. The workflow detects traceable calibration references on a non-motorized microscope, applies the resulting scale to aperture and wire measurements, and uses OpenCV to analyse the sieve images. It also supports optional z-stacks and exports structured data for the customer's existing certification workbook.
We built a closed-loop tracking workflow in ZEN Black that connects INRAE's BIP registration software to microscope control. After each acquisition, the workflow sends the image to BIP, reads the calculated X, Y, and optional Z displacement, checks movement limits, and repositions the stage before the next frame. Tracking images and scientific z-stacks can run at separate cadences, while BIP remains independently maintainable.