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.
Installation
Install the latest stable version by using pip:
pip install qim3dGetting started
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()GUIs can also be launched using the Qim3D CLI:
$ qim3d gui --data-explorerContributing
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.
You can find us at Gitlab: https://lab.compute.dtu.dk/QIM/tools/qim3d
License
This project is licensed under the MIT License.