Notebook gallery

Here is a gallery of Jupyter notebooks containing workflows for MRK imaging analysis. The majority of the notebooks are use cases of ORMIR packages
Note: Notebook standardization using the ORMIR Jupyter Notebook template is work in progress!

Gallery

See below how to explore the notebooks

Tissue image analysis

isq_io_viz.ipynb

Reading, writing, and visualizing .isq images

Coming soon

ITKIOScanco

An ITK module to read and write Scanco microCT .isq files.

Organ image analysis

pyKNEEr

An open and reproducible workflow for knee cartilage segmentation

Launch binder from

image_data_mha.ipynb

Extracts image spacing, size, and pixel type from a group of .mha images

Mechanical analysis

ciclope

Processes micro computed tomography data to generate finite element models

Coming soon

Image data management

subject_data.ipynb

Calculates descriptive statistics for a group of subjects from tabular data

How to explore the notebooks

• The very easy way:

  • Go to binder:
    (Not familiar with Binder? Watch this video!)

  • Open a notebook

  • Run all cells (Cell -> Run all cells) or run one cell at the time sequentially (click on a cell -> Cell -> Run cell)

  • Do not forget to read the narrative of the notebook!

• The easy way:

  • Clone or download the notebook from the GitHub repository (green button code)

  • Open a notebook, run it, and then try it with your own data!
    (If you are not familiar with the Jupyter/Python enviroment, watch this tutorial)