YouScope is free, open-source software for driving automated microscopes. The new release is on its way. With a visual microplate & chip editor, multi-language scripting, closed-loop smart acquisition, FAIR data export, and reproducible remote control.
New capabilities, built on the same open, extendable core that already drives microscopes in labs today.
Turn any layout into a position map you can loop over.
Draw a standard microplate or a custom microfluidic chip, place wells, chambers and features by hand or from a template, and assign imaging positions visually. YouScope turns the drawing into a coordinate map your protocol iterates over. The days of time-consuming, hand-typed stage positions are over.
Acquisition that reacts to what it sees.
Close the loop between imaging and analysis. Modular segmenters find your objects, quantifiers measure what matters, trackers follow them through time. Results feed back to drive the next acquisition. Mix the built-in modules or drop in your own segmenter, quantifier or tracker.
Automate any protocol, in the language you already use.
One console drives it all. Write in modern Python, legacy Jython, MATLAB or JavaScript. YouScope tracks the environment each script runs in, so native and e.g. Cython-backed packages like NumPy or TensorFlow sit right inside your acquisition logic.
Calibrate your optical system, and track its performance over time.
Run your Argolight reference patterns and turn them into quantitative checks with all aquisition settings generated automatically. For example field illumination, distortion and stage accuracy. To ensure today's images stay comparable to last month's.
Turn experiments into archives others can actually reuse.
Export legacy and current projects to open, standard formats such as OME-TIFF, OME-Zarr and RO-Crates. Images, metadata and provenance travel together, FAIR by default.
Configure complex protocols with YouScope's AI assistant faster.
Configure complex protocols with help from an AI assistant. Connect YouScope to an LLM through an API and use it to configure your optical system, set up attached devices and build measurement protocols. The assistant helps turn what you want to measure into a protocol you can run in YouScope reproducibly.
YouScope has driven automated microscopes for over a decade started in 2009, developed in the Computational Systems Biology group at ETH Zurich, D-BSSE, Basel, Switzerland. Learn more about the contributors.
Free and open-source under a dual license Apache 2.0 or LGPL 2.1. Scriptable, plugin-based, and compatible with most present-day automated microscopes. View the code.
The seperation between hardware configuration and abstract imaging protocols allows for reproducibility by design, so an experiment can be re-run or shared exactly as it ran the first time even on different hardware.