QIM3D (Quantitative Imaging in 3D)

qim3D is a Python library for quantitative imaging analysis in 3D. It provides functionality for handling data, as well as tools for visualization and analysis.

This library contains the tools and functionalities of the QIM platform, accessible at https://qim.dk/platform

Installation

Install the latest stable version by using pip:

pip install qim3d

Or clone this repository for the most recent version.

Usage

Some basic funtionalites are descibred here. The full documentation is still under development.

Loading Data

To load image data from a file, use qim.io.load()

import qim3d

# Load a file
vol = qim3d.io.load("path/to/file.tif")

# Load a file as a virtual stack
vol = qim3d.io.load("path/to/file.tif", virtual_stack=True)

Visualize data

You can easily check slices from your volume using slice_viz

import qim3d

img = qim3d.examples.fly_150x256x256

# By default shows the middle slice
qim3d.viz.slice_viz(img)

# Or we can specifly positions
qim3d.viz.slice_viz(img, position=[0,32,128])

# Parameters for size and colormap are also possible
qim3d.viz.slice_viz(img, img_width=6, img_height=6, cmap="inferno")

GUI Components

The library also provides GUI components for interactive data analysis and exploration. The qim3d.gui module contains various classes for visualization and analysis:

import qim3d

app = qim3d.gui.iso3d.Interface()
app.launch()

Contributing

Contributions to qim3d are welcome! If you find a bug, have a feature request, or would like to contribute code, please open an issue or submit a pull request.

License

This project is licensed under the MIT License.