DySTrack - Dynamic Sample Tracking#
DySTrack (“diss track”) is a simple, modular, python-based, open-source automated feedback microscopy tool for live tracking of moving samples like migratory cells or tissues during acquisition.
This example shows the zebrafish posterior lateral line primordium, a highly migratory tissue, as it crawls along the flank of a developing embryo. DySTrack was used to enable autonomous tracking and 3D confocal imaging of the primordium over several hours on a Zeiss LSM980 microscope. (This gif is maximum z-projected and downsampled to limit file size.)#
DySTrack works on common commercial microscopes, with current out-of-the-box
support covering ZEN Black (via MyPiC), ZEN Blue (via Macros),
and NIS Elements (via JOBS). Adaptation to any other microscope control
software that supports basic macros/automation is also possible, and support
for other systems may be added in the future.
The source code for DySTrack is on GitHub, where you may also contribute to DySTrack’s continued development and maintenance. Please raise a GitHub Issue if you encounter a problem with DySTrack or would like to suggest a new feature. Note that the authors cannot guarantee support.
Citing DySTrack
DySTrack was developed by Jonas Hartmann and Zimeng Wu, in collaboration with many others (acknowledged on GitHub). If you are using DySTrack in your research, please cite the preprint:
@article {Wu2025.12.02.691816,
author = {Wu, Zimeng and Voiculescu, Octavian and Mongera, Alessandro and Mayor, Roberto and Wong, Mie and Hartmann, Jonas},
title = {DySTrack: a modular smart microscopy tool for live tracking of dynamic samples on modern commercial microscopes},
elocation-id = {2025.12.02.691816},
year = {2025},
doi = {10.64898/2025.12.02.691816},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/10.64898/2025.12.02.691816v1},
journal = {bioRxiv}
}
Why use DySTrack?#
DySTrack is useful when imaging moving, growing, or drifting samples where the microscope’s limited field of view becomes an issue. Instead of sitting at the microscope all day and all night, or accepting lower quality (reducing magnification to increase the field of view) or lower time-resolution (using tiled/stitched acquisition to cover a larger field of view), DySTrack can be deployed to have the microscope autonomously follow cells or tissues of interest.
Some advantages of DySTrack over other tools include:
Minimal interface with the microscope
Can interface with any microscope control software that has basic macro/automation support
No specialized custom microscope setup or custom control software required
Allows easy switching/reuse of the same image analysis pipeline; no lock-in to vendor ecosystems
Simple and modular python tool
Usable, understandable, and extendable for a large & growing fraction of life scientists
Custom python image analysis pipelines
Python is the de facto standard for both basic and advanced bioimage analysis
DySTrack lets you use it to automate your microscopes!
A word of warning…#
DANGER: USE AT YOUR OWN RISK!
Modern microscopes are expensive machines, and automating them comes with an inherent risk of damage.
Although DySTrack includes some basic precautions and has been extensively tested, and although several labs have been using (prototypes of) DySTrack successfully for years, DySTrack is ultimately a minimal tool that does not offer comprehensive built-in safety features.
We recommend that installation and initial tests be conducted by expert users with experience in microscopy and coding, and that the microscope be monitored during initial tests and when running newly customized pipelines.
Users are advised that the authors provide no warranty of any kind for DySTrack and are not liable for damages of any kind resulting from its use. Note the relevant part of DySTrack’s MIT license:
THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.