Here is a gallery of Jupyter notebooks containing workflows for MRK imaging analysis.
The majority of the notebooks are use cases of
Note: Notebook standardization using the ORMIR Jupyter Notebook template is work in progress!
See below how to explore the notebooks
Tissue image analysis¶
Organ image analysis¶
Image data management¶
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 (
Run all cells) or run one cell at the time sequentially (click on a 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
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)