About CellSeg

What is CellSeg?

CellSeg is a free, open-source Android application for quantitative cell segmentation of microscopy images. It is designed for researchers and field scientists who need rapid, reproducible cell counting without cloud dependencies or specialised desktop hardware.

Key design goals:

• Offline-first — the full segmentation pipeline runs on-device after a one-time model download.
• Quantitative — cell count, confluence %, mean/median cell area, and density are computed per run.
• Privacy-preserving — no analytics, no crash reporters, no data upload in local mode.
• Open — MIT-licensed source code; Cellpose codebase under BSD 3-Clause.

The model: Cellpose cyto3

CellSeg uses the Cellpose cyto3 generalised cell segmentation model, exported to ONNX FP16 format for on-device inference via ONNX Runtime 1.19 with XNNPACK acceleration.

The cyto3 model is part of the Cellpose project led by Carsen Stringer and Marius Pachitariu at HHMI Janelia Research Campus.

Citation

If you use CellSeg in published research, please cite the original Cellpose papers:

Stringer, C., Wang, T., Michaelos, M. & Pachitariu, M. Cellpose: a generalist algorithm for cellular segmentation. Nature Methods 18, 100–106 (2021). https://doi.org/10.1038/s41592-020-01018-x

Pachitariu, M. & Stringer, C. Cellpose 2.0: how to train your own model. Nature Methods 19, 1634–1641 (2022). https://doi.org/10.1038/s41592-022-01663-4

Stringer, C. & Pachitariu, M. Cellpose3: one-click image restoration for improved cellular segmentation. Nature Methods 22, 592–599 (2025). https://doi.org/10.1038/s41592-025-02595-5 (This is the cyto3 model used in CellSeg.)

Pachitariu, M., Rariden, M. & Stringer, C. Cellpose-SAM: superhuman generalisation for cellular segmentation. bioRxiv (2025). https://doi.org/10.1101/2025.04.28.651001 (Used in cloud/HuggingFace inference mode.)

Licences

CellSeg — MIT Licence

MIT License

Copyright (c) 2025–2026 Kemal Yaylali

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

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.

Cellpose codebase — BSD 3-Clause Licence

The Cellpose source code is released under the BSD 3-Clause Licence (Copyright © 2020 Howard Hughes Medical Institute). The full licence text is in the upstream repository at github.com/MouseLand/cellpose/blob/main/LICENSE.

Cellpose cyto3 weights — redistributed with permission

The cyto3 model weights themselves do not have an explicit upstream licence statement. They are redistributed in this app’s ONNX form at huggingface.co/kmlyyll/cellpose-cyto3-onnx with the explicit permission of the upstream authors at HHMI Janelia, granted by Marius Pachitariu (May 2026), under the conditions of:

1. Attribution of the Cellpose papers and project.
2. Licence propagation — this notice must travel with any further redistribution.

For completeness on the upstream chain: Cellpose-SAM (used by the app’s optional cloud mode) sits on top of Segment Anything (SAM) weights. Per Michael Perham (Director, Janelia Innovations & Open Science at HHMI Janelia, May 2026), these upstream SAM weights carry a fully permissive licence that allows commercial applications.

ONNX Runtime — MIT Licence

ONNX Runtime is used for on-device model inference.

MIT License

Copyright (c) Microsoft Corporation

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

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.

Third-party software

The following open-source libraries are used in CellSeg. All are included unmodified. Full licence texts are in the NOTICE file.

The Apache 2.0 Licence can be read at apache.org/licenses/LICENSE-2.0.

Author

Kemal Yaylali yaylali.uk · GitHub: @lynchaos · support@yaylali.uk

Contributing

Contributions are welcome — bug reports, feature requests, and pull requests. Please read CONTRIBUTING.md before opening a pull request.

Disclaimer