Image Analysis II

Introduction to Python/Jython programming languages:

• From ImageJ macro language to Jython programming language in Fiji
• Python basics: syntax, statements, expressions, list, loops, conditional statements, functions
• From Python to Jython: object oriented programming
• Jython main APIs and Classes for Fiji
• Python vs Jython: Pros and cons

Hands-on: practice on a nuclei segmentation macro and comparison with Jython language

• Implementation of nuclei segmentation
• Focus on Regions Of Interest Manager
• Creation of customized Results table

More complex image analysis and Analysis of Multiple Images

Hands-on: nuclei segmentation with spots count and intensity measurement

• Bio-formats handling
• User interaction
• Multiple channel handling
• Parent-children objects handling
• Multiple Results Table management
• Multiple images analysis

Introduction to machine learning and deep learning in image analysis

• Theoretical introduction about machine learning and deep learning
• Machine learning as tool for semantic segmentation/pixel classification
• Deep Learning as tool for image restoration and instance segmentation

Hands-on: Semantic segmentation/pixel classification with Labkit

Image restoration and instance segmentation using Deep Learning in Python

• Introduction to Jupyter (Python) notebooks and their use in cloud with ZeroCostDL4Mic
• Deep Learning algorithms for image restoration and instance

Hands-on: Image restoration and nuclear segmentation with Deep Learning algorithms

• Image restoration using Noise2Void algorithm; model training and application using Jupiter notebooks in ZeroCostDL4Mic
• Nuclear segmentation using 2D and 3D Stardist using Jupyter notebooks in ZeroCostDL4Mic

Segmentation in tissues using Stardist with QuPath software:

• Introduction to QuPath for tissue sections analysis
• Cell segmentation in tissues

Hands-on: Cell segmentation in tissues using Stardist and cell-type classification in different populations

Cell segmentation using Cellpose software in Python:

• Introduction to conda environments and their utility for using local Jupyter (Python) notebooks
• CellPose Deep Learning software for cell and nuclear segmentation

Hands-on: Segmentation of cells and nuclei using CellPose and evaluation of cytoplasmic signal using local Jupyter notebooks