cytounet 0.1.0

A Keras-Tensorflow based Unet for Cyto Image Segmentation

---

Installation

To install:

git clone https://github.com/Nelson-Gon/cytounet.git

Or:

pip install git+https://github.com/Nelson-Gon/cytounet.git

Import

from cytounet.model import *
from cytounet.data import *
from cytounet.augmentation import *

Detailed Sample Usage

Please see the following examples:

• Typical Pipeline available here

• A biological example showing segmentation of DIC images of embryos available here

For more examples or to add your own, please see the examples folder.

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.

• Single class segmentation

• Grayscale images

• Model Validation

• Multi-class segmentation

• Colored image input

• COCO Datasets

• CSV Based Annotations

• XML Based Annotations

To raise an issue or question

Please raise an issue here if you have any discussion, criticism,

or bug reports.

Thank you very much.

---

References

• Mouse Embryos Dataset obtained from Broad Bioimage Benchmark Collection. Source.

• Red Blood Cell Images provided by Anne Carpenter and Roger Wiegand, available here

Credits

• This repository started out as a clone of zhuxihao's original unet implementation.

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 from the original implementation here.

• The Unet algorithm was introduced by Ronneberger et al. in their paper.