2.format_training_data

2. Format Training Data

In this module, we associate features extracted from labeled frames with their Mitocheck-assigned phenotypic class label. After extracting the features from these labeled frames with idrstream, we associate the center coordinates of cells from features.samples.txt with their idrstream-derived outlines to assign a phenotypic class (as assigned by Mitocheck) to cell features.

Note: We replace Shape1 and Shape3 with binuclear and polylobed respectively (their corresponding classes). See #16 for more details.

Step 1: Format Training Data

Use the commands below to format the training data:

# Make sure you are located in 2.format_training_data
cd 2.format_training_data

# Activate mitocheck_data conda environment
conda activate mitocheck_data

# Format data
bash format_training_data.sh