readme.md

This is the course materials for the 3D segmentation workshop

Please look to Crick_IA_setup.md to install the conda environment that we will be using in class. We will go over this in class

Please download all these files to a location on your harddrive that is easy to find repeatedly:

Environment File:

• Crick_IA.yml - Conda environment for the 3D Segmentation workshop

Demo Images

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

Demo Code

• StarDist_Demo.ipynb - StarDist Segmentation Jupyter Notebook
• CellPose_Demo_Sept24.ipynb - CellPose Segmentation Jupyter Notebook
• Data_Analysis.ipynb - Data Analysis Jupyter Notebook

Presentation

• 3D_Segmentation.pptx Course slides
• conda-cheatsheet.pdf Conda Cheat Sheet