medical-imaging-guide

Medical Imaging Guide

A skill for applying deep learning to medical image analysis in research settings. Covers common imaging modalities, preprocessing pipelines, architecture selection for classification and segmentation tasks, handling small datasets with transfer learning and data augmentation, evaluation metrics specific to medical imaging, and regulatory and ethical considerations for clinical translation.

Imaging Modalities and Data Characteristics

Common Modalities in Research

Modality Overview:

X-ray / Radiography:
  - 2D grayscale images
  - Resolution: typically 2000x2000 to 4000x4000 pixels
  - Format: DICOM (.dcm)
  - Common tasks: pneumonia detection, fracture detection,
    cardiomegaly screening
  - Dataset examples: CheXpert, MIMIC-CXR, NIH ChestX-ray14

CT (Computed Tomography):
  - 3D volumetric data (stack of 2D slices)
  - Resolution: 512x512 per slice, 50-500+ slices
  - Format: DICOM series, NIfTI (.nii.gz)
  - Common tasks: lung nodule detection, organ segmentation,
    COVID-19 screening
  - Dataset examples: LUNA16, DeepLesion, TotalSegmentator

MRI (Magnetic Resonance Imaging):
  - 3D volumetric, multiple sequences (T1, T2, FLAIR, DWI)
  - Resolution: 256x256 to 512x512 per slice
  - Format: DICOM, NIfTI
  - Common tasks: brain tumor segmentation, cardiac analysis,
    knee injury classification
  - Dataset examples: BraTS, ACDC, fastMRI

Histopathology:
  - Whole slide images (WSI), extremely large
  - Resolution: 100,000x100,000+ pixels at highest magnification
  - Format: SVS, TIFF, NDPI (vendor-specific)
  - Common tasks: cancer grading, mitosis detection,
    tissue classification
  - Dataset examples: Camelyon16/17, TCGA, PANDA

Retinal Imaging (Fundoscopy / OCT):
  - 2D color fundus or 3D OCT volumes
  - Common tasks: diabetic retinopathy grading, glaucoma detection
  - Dataset examples: EyePACS, MESSIDOR, REFUGE

Preprocessing Pipeline

Standard Preprocessing Steps

import numpy as np

def preprocess_medical_image(image, modality="xray"):
    """
    Standard preprocessing pipeline for medical images.

    Steps vary by modality but typically include:
    1. Intensity normalization
    2. Resizing/resampling
    3. Windowing (for CT)
    4. Artifact removal
    """
    if modality == "ct":
        # CT windowing: map Hounsfield Units to display range
        # Lung window: center=-600, width=1500
        # Soft tissue: center=40, width=400
        window_center = -600
        window_width = 1500
        lower = window_center - window_width // 2
        upper = window_center + window_width // 2
        image = np.clip(image, lower, upper)
        image = (image - lower) / (upper - lower)

    elif modality == "xray":
        # Normalize to [0, 1] range
        image = image.astype(np.float32)
        image = (image - image.min()) / (image.max() - image.min() + 1e-8)

    elif modality == "mri":
        # Z-score normalization (per-volume)
        # Exclude background (zeros) from statistics
        mask = image > 0
        if mask.any():
            mean_val = image[mask].mean()
            std_val = image[mask].std()
            image = (image - mean_val) / (std_val + 1e-8)

    return image


def resize_with_spacing(image, original_spacing, target_spacing):
    """
    Resample 3D medical image to uniform voxel spacing.
    Essential for CT/MRI where slice thickness varies.

    Args:
        image: 3D numpy array
        original_spacing: (z, y, x) voxel sizes in mm
        target_spacing: desired (z, y, x) voxel sizes in mm
    """
    from scipy.ndimage import zoom

    resize_factor = [
        orig / target
        for orig, target in zip(original_spacing, target_spacing)
    ]
    resampled = zoom(image, resize_factor, order=1)
    return resampled