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Image Analyis with Napari and Python (Helmholtz Imaging Summer Academy 2022)
Image analysis with Python and Napari - A Helmholtz Imaging Summer Academy 2022
Introduction to Napari for image analysis
Installation
Exercise: Interactive pixel and object classification
Introduction to Jupyter Lab
Python code in Jupyter notebooks
Pitfalls when working with Jupyter notebooks
Using Jupyter Notebooks and Napari
Using Napari to visualize and interact with images
Segmentation Workflow Example with 3D Data
Batch Segmentation Workflow Example
Image Processing
Histogram
Binarization
Image Filters
Morphological Image Processing
Image segmentation
Image segmentation
Voronoi-Otsu-labeling
Label image visualization
Seeded watershed for membrane-based cell segmentation
Label image refinement
Feature extraction
Quantitative image analysis using scikit-image
Quantitative image analysis using SimpleITK
Working with tabular data
Introduction to working with DataFrames
Appending tables
Handling NaN values
Parametric maps
Interacting with measurements in Napari
Plotting Data with Seaborn
Plotting Data with Python
Introduction to Seaborn
Plotting Distributions with Seaborn
Multivariate views
Complex exercise
Complex exercise
Index
