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Pleased to say that Jonas Hartmann (bs-less) and I have finally released DySTrack (“diss track”) - Dynamic Sample Tracking. It’s a Python-based, modular tool that brings smart microscopy to everyday imaging on commercial systems. Preprint: www.biorxiv.org/content/10.6... [1/6]

Video

6mo

Zimeng Wu

We include example pipelines for: 🐟 migrating zebrafish pLLP 🐟 zebrafish neuromast drift correction 🐣 chick Hensen’s node (pictured) All easy to adapt to your own system. [4/6]

6mo

The result: Your microscope can follow moving or drifting samples on its own with no vendor lock-in, no rewriting control software and no massive frameworks to learn. We provide integration for Zeiss LSM880, LSM980 and Nikon scopes that have JOBS. [3/6]

I always get weirdly sad setting up/collecting my fish/embryos for the last time every year and hope that they have a happy holidays too

5mo

Big thanks to Nick S. from @zeiss-microscopy.bsky.social and Rob T. from @healthcare.nikon.com for help with integration development. Also the UCL facility for microscopy support. And of course our co-authors Octavian, @mongeralab.bsky.social, @mayorlab.bsky.social and @miewong.bsky.social. [6/6]

If you’ve wanted a low-barrier entry into smart microscopy then this is it. Open-source, documented, and ready for feedback & contributions. Check out the GitHub repo here: github.com/WhoIsJack/Dy... [5/6]

The core idea is simple: DySTrack lets you keep using Zeiss/Nikon software for acquisition while running any Python image analysis you want in the loop. It watches prescans -> runs your analysis -> updates stage coords automatically. [2/6]

6mo

DySTrack is officially published!: doi.org/10.1242/jcs.... If anyone is keen on using it feel free to reach out as we are more than happy to help and demo if need be!

Zimeng Wu

6mo

Zimeng Wu

7d

DySTrack: a modular smart microscopy tool for live tracking of dynamic samples on modern commercial microscopes https://www.biorxiv.org/content/10.64898/2025.12.02.691816v1

Zimeng Wu

6mo

We are particular fans of DySTrack (www.biorxiv.org/content/10.6...) by @zimengwu33.bsky.social & Jonas Hartmann at UCL for live tracking of dynamic samples & WaveOrder (arxiv.org/abs/2412.097...) by @mattersoflight.bsky.social et al as a wave-optical framework for scalable biological microscopy 🐟🔬

Zimeng Wu

5mo

Summary: DySTrack is an easy-to-use open-source tool that bridges standard microscope control software with the Python image analysis ecosystem to enable automated tracking of moving, drifting, or gro...

doi.org

DySTrack – a modular smart microscopy tool for live tracking of dynamic samples on modern commercial microscopes

6mo

Pleased to say that Jonas Hartmann (bs-less) and I have finally released DySTrack (“diss track”) - Dynamic Sample Tracking. It’s a Python-based, modular tool that brings smart microscopy to everyday imaging on commercial systems. Preprint: www.biorxiv.org/content/10.6... [1/6]

Video

Zimeng Wu

bioRxivpreprint

Zebrafish Rock!