Image data visualization case studies

In the following sections you’ll find a collection of Jupyter notebook examples involving scientific image processing and analysis in Python and visualization in Napari. To run these notebooks on your computer and edit them, follow the instructions in the Getting Started section.

n-D Image data visualization in Napari

Introduction to the Napari viewer and segmentation of a 3D CT scan of a granular material sample using the watershed transform.

Cell detection and tracking

Detection, tracking, and visualization of dividing cell nuclei in a timeseries.

Skeleton analysis of a drosophila trachea

Analysis of the elongated branching structure of a drosophila trachea in a 3D confocal image using the Skan package.

Lungs convex hull detection

Segmentation of the convex hull of the lungs of a mouse in a CT scan (3D).

Annotating triangular crystallites

Interactive annotation of triangular crystallites and visualization of their orientation distribution.

Digital image correlation

Registration of two 3D images by the optical flow method using the spam package.

Cell nuclei detection

Deep learning based segmentation of cell nuclei in H&E images using StarDist.