Tools used for this workshop

This workshop uses Jupyter Notebooks, Napari, Segment Anything (SAM), Cellpose, Stardist and Albumentations among other tools. In addition the following other projects are used.

tnia-python - This is a general utility project for image processing including deep learning utilities.

easy-augment-batch-dl A plugin to perform deep learning on small to medium sized image sets with UNETs, Cellpose, Stardist, SAM and friends. In particular this plugin is useful for performing deep learning with a small number of labels and augmentation, and experimenting with different deep learning frameworks.

segment-everything - This contains utilities for rendering and training prompt-based and overlapping segmentation models (like SAM).

napari-segment-everything - This is a Napari GUI for segment-everything

Some examples may be ‘under construction’