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Trailer: Bio-image Analysis with Python
Setting up your computer
Python basics
Writing sustainable code
Image analysis basics

Image file formats

Machine learning basics

Image visualization in 3D

Image filtering

Image deconvolution

Spatial transforms

Image segmentation

Machine learning for image segmentation

Deep Learning based image segmentation

Large Language Vision Models

Segmentation post-processing

Surface processing

Feature extraction

Neighborhood analysis in tissues

Cell classification

Algorithm validation

Explainable AI / SHAP

Simulating data

Advanced python programming

GPU accelerated image processing

Graphical user interfaces

Tiled image processing

Batch processing

Timelapse analysis

Parameter optimization

Prompt engineering

Workflow automation

Tabular data wrangling

Querying databases

Descriptive statistics

Data visualization

Site Navigation

Trailer: Bio-image Analysis with Python
Setting up your computer
Python basics
Writing sustainable code
Image analysis basics

Image file formats

Machine learning basics

Image visualization in 3D

Image filtering

Image deconvolution

Spatial transforms

Image segmentation

Machine learning for image segmentation

Deep Learning based image segmentation

Large Language Vision Models

Segmentation post-processing

Surface processing

Feature extraction

Neighborhood analysis in tissues

Cell classification

Algorithm validation

Explainable AI / SHAP

Simulating data

Advanced python programming

GPU accelerated image processing

Graphical user interfaces

Tiled image processing

Batch processing

Timelapse analysis

Parameter optimization

Prompt engineering

Workflow automation

Tabular data wrangling

Querying databases

Descriptive statistics

Data visualization

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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
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
Explainable AI / SHAP
- Pixel classification explained with SHAP
- Explaining Object classification using SHAP
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

Colocalization

Colocalization#

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Object classification with APOC and SimpleITK-based features

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Counting nuclei according to expression in multiple channels

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

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