aicsmlsegment 0.0.2

Scripts for ML structure segmentation.

### Installation

1. create a conda environment:

`bash conda create --name mlsegmenter python=3.6 `

2. activate your environment and do the installation within the environment:

`bash source activate mlsegmenter `

3. Install Pytorch

Go to [PyTorch website](https://pytorch.org/get-started/locally/), and find the right installation command for you.

• we use version 1.0 (which is the stable version at the time of our development)

• we use Linux (OS), Conda (package), python 3.6 (Language), CUDA=9.0 (Question about CUDA? see [setup CUDA](./docs/check_cuda.md)). So, the installation command for us is

`bash conda install pytorch torchvision -c pytorch `

4. Install Allen Cell Segmenter (deep learning part)

`bash git clone https://aicsbitbucket.corp.alleninstitute.org/scm/assay/aics-ml-segmentation.git cd ./aics-ml-segmentation pip install -e . `