Citing mosaic and the work it builds on¶
Mosaic is a platform. Most results it produces were produced by somebody else's method, running in somebody else's software, and mosaic's contribution is that the data, the parameters, and the runs were organized reproducibly around it.
The rule
Cite the tools that produced the science first, as their authors ask. Cite mosaic second, as the platform that organized the data and the runs.
If you tracked with SLEAP through mosaic, your methods section cites SLEAP for the pose tracking and mosaic for the pipeline. Not the other way around, and not mosaic alone.
What you owe, by kind¶
Every component mosaic draws on falls into one of four kinds, and what you owe depends only on the kind.
| Kind | What it means | What to cite |
|---|---|---|
| runs | Mosaic executes it, or downloads and runs its weights. | Cite it. You may not realize you used it, so this is the kind to check. |
| imports | You ran it yourself; mosaic reads its output. | Cite it if your data came from it. You already know whether it did. |
| implements | Mosaic implements the published method in its own code. There is no package to cite. | Cite the method. |
| builds on | Foundation mosaic is built from. | No citation expected. |
The distinction that matters is between the first two. Something you import (DeepLabCut, BORIS, CVAT) you chose and ran yourself, so you already know it belongs in your methods section. Something mosaic runs may have been a default you never typed, which is why this page exists.
To see what a component is and what its authors ask, NOTICE records the origin, license and requested citation of the tools mosaic drives, the third-party code it incorporates and the model weights it can fetch. The feature reference describes what each feature computes.
The short answer¶
For most projects:
- Your tracker or pose estimator. Whatever produced the pose data.
- Anything mosaic runs that you turned on. Behavior models, identity backbones, detectors.
- The method behind any analysis your paper names. If your methods section says "wavelet spectrogram and t-SNE embedding", cite the method, not only the libraries.
- Mosaic.
Citing mosaic itself¶
The repository carries a CITATION.cff, which GitHub renders as a "Cite this
repository" entry. A software DOI will be added once the project is archived.
Until then, cite the repository and the mosaic version recorded in your run's
params.json as _mosaic_version.
Mosaic does not require citation. It asks for it on the same terms it asks you to cite everything else.
A methods paragraph¶
Adapt this, filling in from your run's params.json:
Pose tracks were produced with {tracker} {version} [ref] and standardized and analyzed with mosaic {version} [ref]. {Analysis} followed {method} [ref], using {key parameters}. Each analysis step is addressed by a content hash over its parameters and inputs, recorded in the accompanying dataset.
Two things this page is not¶
It is not the licensing page. Whether you may use a component, and under what terms, is a different question with different answers. keypoint-MoSeq prohibits commercial use, TRex requires a paid license for company use, and MegaDescriptor's weights are non-commercial. NOTICE states those terms.
Two components make attribution a license condition rather than a courtesy, and both are called out in NOTICE: keypoint-MoSeq, whose license requires acknowledging Harvard as the provider, and MegaDescriptor, whose CC-BY-NC terms require attribution.
It is not a complete bibliography of the field. It covers what mosaic actually draws on. Methods mosaic does not implement are not here, however relevant.