embryoseg 2.2.5

SmartSeed Segmentation for animal embryonic cells.

EmbryoSeg

Segmentation tool for multiple touching mouse embryo cells

Installation

This package can be installed by

pip install --user embryoseg

If you are building this from the source, clone the repository and install via

git clone https://github.com/kapoorlab/embryoseg/

cd embryoseg

pip install --user -e .

# or, to install in editable mode AND grab all of the developer tools
# (this is required if you want to contribute code back to NapaTrackMater)
pip install --user -r requirements.txt

Pipenv install

Pipenv allows you to install dependencies in a virtual environment.

# install pipenv if you don't already have it installed
pip install --user pipenv

# clone the repository and sync the dependencies
git clone https://github.com/kapoorlab/embryoseg/
cd embryoseg
pipenv sync

# make the current package available
pipenv run python setup.py develop

# you can run the example notebooks by starting the jupyter notebook inside the virtual env
pipenv run jupyter notebook

Access the example folder and run the cells.

Algorithm

Example

Requirements

• Python 3.7 and above.

License

Under MIT license. See LICENSE.

Authors

• Varun Kapoor [e-mail]
• Leo Guginard