Metadata-Version: 2.1
Name: cytounet
Version: 0.2.0
Summary: Deep Learning based Cell Segmentation
Home-page: http://www.github.com/Nelson-Gon/cytounet
Author: Nelson Gonzabato
Author-email: gonzabato@hotmail.com
License: MIT
Download-URL: https://github.com/Nelson-Gon/cytounet/archive/v0.2.0.zip
Description: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3928919.svg)](https://doi.org/10.5281/zenodo.3928919)
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        ---
        
        
        **Installation**
        
        From `PyPI`:
        
        ```
        
        pip install cytounet
        
        ```
        
        
        From source or to use without installing locally:
        
        ```
        git clone https://github.com/Nelson-Gon/cytounet.git
        # proceed with usual source build procedure
        
        ```
        
        Or:
        
        ```python
        
        pip install git+https://github.com/Nelson-Gon/cytounet.git
        
        ```
        
        **Import**
        
        ```python
        
        from cytounet.model import *
        from cytounet.data import *
        from cytounet.augmentation import *
        
        ```
        
        **Detailed Sample Usage**
        
        Please see the following examples:
        
        
        * [Predicting Embryonic DIC Image Labels with Keras](https://www.kaggle.com/gonnel/predicting-embryonic-dic-image-labels-with-keras)
        
        [![nbviewer](https://img.shields.io/badge/view%20on-nbviewer-brightgreen.svg)](https://nbviewer.jupyter.org/github/Nelson-Gon/cytounet/blob/aedf8d52af4e3e9f2cd426de90b4c5dea2a4e11c/examples/embryos_dic.ipynb)
        
        
        
        * Chinese Hamster Ovary [Segmentation](https://github.com/Nelson-Gon/cytounet/blob/ff5ce0c2cc97e35baf1edacbc994661583200884/examples/example_usage.ipynb)
        
        [![nbviewer](https://img.shields.io/badge/view%20on-nbviewer-brightgreen.svg)](https://nbviewer.jupyter.org/github/Nelson-Gon/cytounet/blob/ff5ce0c2cc97e35baf1edacbc994661583200884/examples/example_usage.ipynb)
        
        
        Visually:
        
        ![CHO](https://raw.githubusercontent.com/Nelson-Gon/cytounet/master/examples/example_results.png)
        
        
        For more examples or to add your own, please see the examples [folder](https://github.com/Nelson-Gon/cytounet/blob/master/examples).
        
        **Is it supported?**
        
        A checked box indicates support. You can either add more feature requests here or tackle unchecked boxes and make
        a pull request to add such support. 
        
        - [ ] Custom Number of Layers
        
        - [x] Single class segmentation
        
        - [x] Grayscale images
        
        - [x] Model Validation
        
        - [ ] Multi-class segmentation
        
        - [ ]  Colored image input
        
        - [ ] COCO Datasets 
        
        - [ ] CSV Based Annotations
        
        - [ ] XML Based Annotations 
        
        **Frequently Asked Questions**
        
        Please read our Wiki [Pages](https://github.com/Nelson-Gon/cytounet/wiki)
        
        **To raise an issue or question**
        
        If the [wiki](https://github.com/Nelson-Gon/cytounet/wiki) does not answer your question,
        please raise a new [issue](https://github.com/Nelson-Gon/cytounet/issues). You can also open an issue if you have any discussion, criticism,
        or bug reports. 
        
        Thank you very much. 
        
        ---
        
        **References**
        
        * Mouse Embryos [Dataset obtained](https://github.com/Nelson-Gon/cytounet/tree/master/examples/BBBC003_v1) from Broad Bioimage Benchmark Collection.
        [Source](https://data.broadinstitute.org/bbbc/BBBC003/).
        
        * Red Blood Cell [Images](https://github.com/Nelson-Gon/cytounet/tree/master/examples/BBBC009_v1) provided by Anne 
        Carpenter and Roger Wiegand, available [here](https://data.broadinstitute.org/bbbc/BBBC009/)
        
        * Chinese Hamster Ovary [Cells](https://github.com/Nelson-Gon/cytounet/tree/master/examples/BBBC030_v1) provided by 
        Koos et al.([2016](https://bbbc.broadinstitute.org/BBBC030))
        
        **Credits**
        
        * This repository started out as a clone of [zhixuhao](https://github.com/zhixuhao)'s  original 
        unet [implementation](https://github.com/zhixuhao/unet/).
        
        This repository has considerably diverged from the original implementation hence the need
        to distribute it separately. 
        
        This decision was taken in part due to the relative inactivity of the original implementation which would have made
        it harder to collaborate. Please take a look at the list of [changes](https://github.com/Nelson-Gon/cytounet/blob/master/changelog.md) 
        from the original implementation. 
        
        * The Unet algorithm was introduced by Ronneberger et al. in their [paper](http://lmb.informatik.uni-freiburg.de/people/ronneber/u-net/).
        
        
        
        
Keywords: keras tensorflow images image-analysis deep-learning biology
Platform: UNKNOWN
Requires-Python: >=3.6
Description-Content-Type: text/markdown
