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
ITKIOScanco
Organ image analysis¶
pyKNEEr
image_data_mha.ipynb
Mechanical analysis¶
ciclope
Image data management¶
subject_data.ipynb
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)
-