File Descriptions

File Descriptions

Here are descriptions of the files included in the ScaleFEx git repository

Main Directory

Local-Specific Files

scalefex_main.py:

scalefex_utils.py:

tests/parameters_test.yaml

tests/test_scalefex_main.py

tests/test_scalefex_utils.py

AWS-Specific Files

AWS_scalefex_main.py:

AWS_scalefex_extraction.py:

AWS_requirements.txt

Other Files

parameters.yaml

pytest.ini

setup.py

__init__.py

.gitignore

Modules (separated by function)

Each of these module directories contains:

1. README.md: description of functionality of code within directory
2. setup.py: script for installing module via pip
3. __init__.py: required file for local namespace package installation
4. tests/: unit tests and testing data each function implemented in the main .py files

Nuclei_segmentation

This directory contains code for segmenting nuclei from the stained nuclei channel (e.g., DAPI, Hoechst)

1. nuclei_location_extraction.py:

ScaleFEx_from_crop

This directory contains code for extracting ScaleFEx features from a single-cell, multi-channel image crop

1. compute_ScaleFEx.py:
2. compute_measurements_functions.py

data_query

This directory contains code for querying data from a local directory or an AWS S3 bucket, depending on the user's specfication

1. query_functions_local.py
2. query_functions_AWS.py

Quality_control_HCI

This directory contains code for computing site-level image quality metrics to help users assess potential issues with their dataset (e.g., blur, exposure, etc)

1. compute_global_values.py