3D segmentation

10th & 11th September 2025

Slides

• Session 1: Introduction to 3D segmentation and installation – Sara Salgueiro Torres; slides
• Session 2: Introduction to napari and conda env creation - Rocco D’Antuono; slides

Download

Please download the files to a location on your hard drive that is easy to find!

Demo data

• Image_Set_1_001.tif - 2D Nucleus example
• 3d_monolayer_xy1_ch2.tif - 3D Nucleus example

Code

During the second part of the workshop, we will be using the following notebooks

• Watershed_3DSegmentation.ipynb - Classical watershed segmentation with scikit-image - Jupyter notebook
• StarDist_Demo.ipynb - StarDist Segmentation Jupyter Notebook
• Data_Analysis.ipynb - Data Analysis Jupyter Notebook

Set up the conda environment

For this module, we will be using jupyter notebooks to run our 3D segmentation with classical watershed algorithm and StarDist deep learning model, and analyse the resulting data.

To do so, we will create a conda environment during the workshop following these instructions.