API Reference

This section provides detailed documentation for all modules, classes, and functions.

The package is organized into several main modules:

Core Modules

cellmil.cli

cellmil.config.python

cellmil.data

cellmil.datamodels

cellmil.dataset

cellmil.features

cellmil.interfaces

cellmil.models

cellmil.segmentation

cellmil.graph

cellmil.utils

cellmil.statistics

cellmil.visualization

Package Structure

The cellmil package is structured as follows:

cellmil/
├── cli/                    # Command-line interface tools
│   ├── patch_extraction.py
│   ├── cell_segmentation.py
│   ├── feature_extraction.py
│   └── ...
├── models/                # Deep learning models
│   ├── enconders/         # Image encoders
│   ├── segmentation/      # Cell segmentation models
│   └── mil/               # Multiple instance learning models
├── data/                  # Data processing utilities
├── datamodels/            # Data models
├── dataset/               # Dataset utilities
├── features/              # Feature extraction modules
├── mil/                   # Multiple instance learning modules
├── interfaces/            # Configuration interfaces
├── segmentation/          # Cell segmentation utilities
├── graph/                 # Graph utilities
├── visualization/         # Visualization tools
├── tests/                 # Unit tests [Almost useless]
└── utils/                 # Utility functions

Quick Access

Common Classes and Functions

Data Processing:

Segmentation Models:

MIL Models:

  • cellmil.models.mil.CLAM_SB - CLAM single branch

  • cellmil.models.mil.CLAM_MB - CLAM multi branch

  • cellmil.models.mil.MIL_fc - Standard MIL with Max pooling (Binary Classification)

  • cellmil.models.mil.MIL_fc_mc - Standard MIL with Max pooling (Multi-class Classification)

  • cellmil.models.mil.TransMIL - Transformer MIL with PPEG

  • cellmil.models.mil.HistoBistro - HistoBistro MIL

Feature Extraction:

  • cellmil.features.Extractor - Base feature extractor interface

Visualization: