https://github.com/cxhernandez/cellcount
A Convolutional Neural Network for Segmenting and Counting Cells in Microscopy Images
https://github.com/cxhernandez/cellcount
biology computer-vision python pytorch segmentation
Last synced: 7 months ago
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A Convolutional Neural Network for Segmenting and Counting Cells in Microscopy Images
- Host: GitHub
- URL: https://github.com/cxhernandez/cellcount
- Owner: cxhernandez
- License: mit
- Created: 2017-05-18T17:27:29.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2019-04-16T14:50:36.000Z (over 6 years ago)
- Last Synced: 2025-03-18T06:11:42.940Z (7 months ago)
- Topics: biology, computer-vision, python, pytorch, segmentation
- Language: TeX
- Homepage:
- Size: 4.06 MB
- Stars: 58
- Watchers: 8
- Forks: 23
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# cellcount
This is a Python 3.4+ project that uses PyTorch v0.4.1.
## Example Usage
After installing via `python setup.py install`, you can use the command-line commands to download an example BBBC dataset, train the feature pyramid network (FPN), and finally train the fulll end-to-end cell counting network:
```
$ cell_count download --dataset bbbc005
$ cell_count train_fpn --dataset path/to/bbbc005
$ cell_count train --dataset path/to/bbbc005
```
## Citing
If you find this software useful for your work, please cite:
```bibtex
@article{cellcount,
Author = {Carlos X. Hernández and Mohammad M. Sultan and Vijay S. Pande},
Title = {Using Deep Learning for Segmentation and Counting within Microscopy Data},
Year = {2018},
Eprint = {arXiv:1802.10548},
}
```