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Bio-image Analysis Notebooks

Basics

Trailer: Bio-image Analysis with Python
Setting up your computer
Python basics
Writing sustainable code
Image analysis basics
Image file formats
Remote files
Machine learning basics
Image visualization in 3D
Image filtering
Image deconvolution
Spatial transforms

Image Segmentation

Image segmentation
Machine learning for image segmentation
Deep Learning based image segmentation
- Image Segmentation with CellPose
- Image segmentation with StarDist
Large Language Vision Models
- Vision Large Language Models for Counting objects
Segmentation post-processing
Blob detection
- Local maxima detection
- Blob detection
Surface processing

Quantitative analysis

Feature extraction
Neighborhood analysis in tissues
Cell classification
Colocalization
Algorithm validation
Simulating data
- Simulation of image formation + image restoration
- Counting cell neighbors in tissues

Advanced techniques

Advanced python programming
GPU accelerated image processing
Graphical user interfaces
Tiled image processing
Batch processing
Timelapse analysis
- Measuring features in a time-lapse dataset
- Cell tracking
Parameter optimization
Prompt engineering

Workflow automation

Workflow automation

Tabular data, plots and statistics

Tabular data wrangling
Querying databases
Descriptive statistics
Clustering
Plotting
Data visualization

Appendix

Glossary
Imprint

Repository
Open issue

.md

Neighborhood analysis in tissues

Neighborhood analysis in tissues#

See also

Spatial organization of Colon Crypts from Second Harmonic Generation (SHG) images of fibrillar collagen of mouse colons
squidpy

previous

Measure distance along a center line

next

Neighborhood definitions

By Robert Haase, Guillaume Witz, Miguel Fernandes, Marcelo Leomil Zoccoler, Shannon Taylor, Mara Lampert, Till Korten, Markus Ankenbrand & add-your-name-here-by-sending-a-pull-request-containing-a-notebook

Copyright: Licensed CC-BY 4.0 and BSD3 unless mentioned otherwise. Contribution and feedback welcome.