MorPheT

An end-to-end framework for cell morphology phenotyping

Installation

The anaconda environment for MorPheT can be installed using environment.yml.

conda env create -f environment.yml

• If above command fails:
  1. Create conda

  conda create -n morphet python=3.7
  

  2. Enter env

  conda activate morphet
  

Install required packages:

make setup.env.x

Other required packages (defined under .gitmodules):

git clone --recurse-submodules -j8 [email protected]:chunglabmit/morphet.git

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GUI Tools (QT-based)

Launch MorPheT GUI

# entrypoint: ./src/gui/MorPheT/main.py
# to launch,
$ make launch.morphet.x

Data Annotator within MorPheT

Media1.mp4

Stand-alone Data Annotator GUI

# entrypoint: ./src/gui/main.py
# to launch,
$ make launch.annotator.x set=[train/val/test]
# SET: 'train', 'val', etc

Model Evaluator GUI

# entrypoint: ./src/gui/evaluator/main.py
# to launch,
$ make launch.evaluator.x

Prediction Visualizer GUI

# entrypoint: ./src/gui/prediction/main.py
# to launch,
$ make launch.predictor.x

Media2.mp4