ctpros 0.0.7

Computed Tomography Processing Registration Open Sourced

ctpros: Computed Tomography Processing & Registration - Open Sourced

A handy graphic user interface (GUI) and application programming interface (API) to apply common imaging techniques to your research images.

Two micro-CT images of a single specimen are shown post-registration of their overlapping region before being stitched.

Summary

This program's goal is to ease the utilization of Python's powerful imaging library in medical imaging research, particularly with micro-computed tomography. By combining raw image data with paired affine matrices to describe their real-world orientations, relationships and scaled metrics can be applied between images of varying resolutions, easing common image processing pipelines. Enabling manipulation of these affine transformations with intuitive dragging and rotating operations allows researchers to better visualize and explore their data.

Index

• Installation
• Usage
• Contributors
• License

Installation

Scripts

Not familiar with Python? Download and run the following script installer for:

• Windows

  The download button is to the right-most side of the file header:

  

• Note: Windows may be careful and prompt you to verify to run the script. Select More Info then Run anyway

Familiar with Python? Just pip install ctpros in your Python 3.7 virtual environment with the below system requirements:

• For all operating systems:
• Python 3.7 64-bit
  • Development is tested against 3.7.9. Use other versions at your own discretion.
• For headless servers utilizing graphics/graphic commands:
  • xvfb
    • X virtual frame buffer to mimic a screen
  • OpenGL
    • Open-sourced graphics library (libgl1-mesa-dev)

Usage

Use either the graphic application for your general visualization and image manipulation needs or use the API for scripting, batching, or specifying pipelines. See below for your use case:

Graphic User Interface

Using one of the installer scripts generates a ctpros.bat in the directory of the installer script. Run the generated ctpros.bat to call the program.

For those familiar with Python, call python -m ctpros from the Python virtual environment in which it is installed.

For detailed controls, see the GUI Controls Guide.

Application Programming Interface

Import ctpros like any other Python module to access the GUI and NumPy-derived image classes. Be sure to use the virtual environment ctpros is installed in to be able to import it.

import ctpros

myaim = ctpros.AIM(shape=(50,50,50),dtype='int16')

See the notebooks for more examples of API usage.

Contributors

See CONTRIBUTING.md for code requirements and structure, pipeline details, and more.

License

GPL 3.0