Below are use cases utitlizing PyImageJ and other packages such as
These examples are available in the PyImageJ repository.
More use cases
Here are additional links to some other examples using PyImageJ in other projects.
The pyimagej-dextr repository uses Deep Extreme Cut (DEXTR) to generate ImageJ ROIs via PyImageJ.
PoreSpy, a collection of image analysis tools used to extract information from 3D images of porous materials, uses some ImageJ filters via PyImageJ.
Some projects at LOCI use PyImageJ to invoke the Image Stitching and SIFT-based image registration plugins of Fiji, together with deep learning for multimodal image registration:
Generate pseudo modality via CoMIR for multimodal image registration
Non-disruptive collagen characterization in clinical histopathology using cross-modality image synthesis
WSISR - Single image super-resolution for whole slide image using convolutional neural networks and self-supervised color normalization
To add your usage of PyImageJ to this list, please submit a pull request!