mitk: Python bindings for MITK

The mitk package exposes the data structures and core utilities of the Medical Imaging Interaction Toolkit (MITK) to Python. It ships as a self-contained wheel that bundles the compiled MITK runtime together with its native dependencies (ITK, VTK, CppMicroServices, DCMTK), so you can pip install it and start working with medical images without building MITK from source.

import mitk
import numpy as np

img = mitk.Image(np.zeros((64, 64, 64), dtype=np.float32), spacing=(1.0, 1.0, 2.5))
img.save("output.nrrd")

loaded = mitk.Image("output.nrrd")
print(loaded.shape, loaded.spacing, loaded.origin)

What this site covers

This site documents the Python surface of MITK: classes, functions, NumPy interop, file I/O, geometry, properties. The wider MITK stack (C++ modules, plugins, the application framework, the BlueBerry plugin system) is documented separately at docs.mitk.org/latest/. Think of this site as the Python facade on that stack.

Getting started

• Installation
  • Requirements
  • Install
  • Verify the install
  • Building from source
• Getting started
  • Creating an image
  • NumPy interop
  • File I/O
  • Geometry
  • Properties
  • Next steps

User guide

• Images
  • Construction
  • Properties
  • NumPy interop
  • Time-resolved data
  • Persistence
• Geometry
  • Accessors on mitk.Image
  • Full geometry objects
  • Time-step / time-point conversion
  • NumPy <-> MITK conventions
• File I/O
  • Read
  • Write
  • Supported formats
• Properties
  • Basic usage
  • Owned vs. provided
  • Thread safety
  • Property key paths
  • Lower-level API
• MxN layout DSL
  • Mental model
  • Build a layout
  • Custom layouts
  • File I/O
  • Inspecting and transforming layouts
  • Groups and links
  • See also

API reference

• API reference
  • Image and pixel types
  • File I/O
  • Geometry
  • Points, vectors, color
  • Properties
  • Multi-label segmentation
  • Exceptions
  • MxN layout DSL

See also

• docs.mitk.org/latest/: the full MITK C++ reference and user manual.

• www.mitk.org: the project homepage.