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 model 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 model was trained by Carsen Stringer, Tim Wang, Michaël Pachitariu, and collaborators 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
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 — BSD 3-Clause Licence
The Cellpose cyto3 model weights and source code are distributed under the BSD 3-Clause Licence:
BSD 3-Clause License
Copyright © 2020 Howard Hughes Medical Institute
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its contributors
may be used to endorse or promote products derived from this software without
specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Model homepage: github.com/MouseLand/cellpose
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.
| Library | Version | Licence | Copyright |
|---|---|---|---|
| Jetpack Compose (UI, Foundation, Material3) | 1.7.x | Apache 2.0 | Google LLC |
| Compose Navigation | 2.8.x | Apache 2.0 | Google LLC |
| AndroidX Room | 2.6.x | Apache 2.0 | Google LLC |
| AndroidX DataStore (Proto) | 1.1.x | Apache 2.0 | Google LLC |
| AndroidX Security Crypto | 1.1.x | Apache 2.0 | Google LLC |
| CameraX (core, camera2, lifecycle, view) | 1.4.x | Apache 2.0 | Google LLC |
| Hilt (Dagger Android) | 2.51.x | Apache 2.0 | Google LLC |
| Protocol Buffers (protobuf-javalite) | 4.x | BSD 3-Clause | Google LLC |
| Moshi (core + Kotlin codegen) | 1.15.x | Apache 2.0 | Square, Inc. |
| Retrofit | 2.11.x | Apache 2.0 | Square, Inc. |
| OkHttp | 4.12.x | Apache 2.0 | Square, Inc. |
| Coil (compose) | 2.7.x | Apache 2.0 | Coil Contributors |
| Timber | 5.0.x | Apache 2.0 | Jake Wharton |
| Google Tink (via Security Crypto) | 1.x | Apache 2.0 | Google LLC |
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.