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 🐟🔬
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
I’m glad I’m not the only one then!
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.
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Thank you!!
I’m not quite sure I understand the question - maybe you could elaborate? The major benefit, however, of DySTrack is that you can correct/follow on the fly during acquisition rather than doing anything post!
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...
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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.
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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.
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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.
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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...
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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
My timely return to social media - just ahead of something fun we’re releasing next week! Until then here’s a movie of the zebrafish pLLP migrating past motor neurons and under the spinal cord as a teaser.
Thought I was being really novel when I designed and 3D printed this mold for zebrafish transplants based on the microinjection one, but found out today it already exists…
Bottom: my PLA mold that’s bent from warm agarose
Top: a very kind (more robust looking) gift from @mongeralab.bsky.social
BIOIMAGE ANALYSTS ASSEMBLE!!!
#CBIAS2025
What a fun #CBIAS2025 !!
Courtney @courtneyl7a7.bsky.social has written a lovely piece on this wonderful community initiative we’ve been running for 5 years at UCL - have a read! And follow @biig-ucl.bsky.social !
Our second perspective talk was by Rob Tetley from Nikon Instruments with beautiful example movies developmental dynamics across scales sharing his experience in making the most of resonant scanning confocal imaging.
