QIM Notebooks

This repository contains a curated list of Jupyter Notebooks suitable for serveral tasks related to QIM and Image analysis in general.

Guidelines

Header

The first cell of the notebook should follow the pattern:

# Title of the notebook
Notebook author: Author name (author@email.dk)

Short paragraph that describes the contents of the Notebook.

## Dependencies
Explain how to install non-standard libraries that are needed for the notebook to run, or point to resources.

## Reference this work
In case the main library used for the notebook is part of a publication, the reference should be inserted here.

The reference can be created using the Qim Platform API, that follows this pattern: https://platform.qim.dk/qim-api/reference/<doi address>

For example, accessing the address https://platform.qim.dk/qim-api/reference/10.1109/CVPRW59228.2023.00456 will give you the markdown text for this particular DOI. It can then be easily copied and pasted into the jupyter notebook.

Location

Notebooks should be placed according to their intended usage. New directories can be suggested, but the current structure is the following:

.
├── analysis
│   ├── fiber_tracking
│   └── structure_orientation
├── data
├── detection
├── reconstruction
│   └── phase
├── resources
│   ├── img2d
│   ├── img3d
│   └── libs
├── segmentation
└── visualization

The resources directory should not contain Notebooks, but any data that is required for other Notebooks to run.

Small python libraries can be located in the libsdirectory. And they can be imported by adding the directory to the path:

import sys
sys.path.append("../../resources/libs/")

Contributors

Huge thanks to all the contributors of the Notebook Library!

• Aleksandar Lukic
• Christian Kento Rasmussen
• Felipe Delestro
• H. Martin Kjer
• J. Miguel Valverde
• Kumari Pooja
• Oskar Kristoffersen
• Peter Winkel Rasmussen
• Thorbjørn Erik Køppen Christensen
• Vedrana Andersen Dahl
• Viktor Nikitin