SmartSeed Segmentation for animal embryonic cells.
Project description
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 randomaccessiblekapoor@gmail.com
- Leo Guginard
Project details
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