Using vEM data with napari and EMPANADA – practical

Trainer: Ryan Conrad, Kedar Narayan, Simone Weyend, Andrii Iudin, Osman Salih, and Sriram Sundar Somasundharam

This session was a part of the 2023 iteration of this course.

Overview: 

This session provides a hands-on demonstration of how to run, finetune, and train deep learning models for the segmentation of organelles and other structures in 2D and 3D electron microscopy datasets. In addition, the practical covers the basics of annotating semantic, instance segmentation data and tools for rapidly proofreading a model’s predictions.

Learning objectives:

After this session you should be able to:

• Create a deep learning model for analysis for segmentation of a curated bioimage dataset

Materials:

• Tutorial: https://empanada.readthedocs.io/en/latest/plugin/tutorials.html#finetuning-an-existing-model