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Code of Conduct
Setup
Modules
Tool installation
Digital image basics
Thresholding
Morphological filters
Connected component labeling
Object shape measurements
Spatial calibration
N-dimensional images
Data types
Image data formats
Big image data formats
OME-TIFF
Remote (image) data access
OME-Zarr
Template
Quantitative image inspection and presentation
Correlative image rendering
Volume slicing
Projections
Volume rendering
Segmentation
Nuclei segmentation and shape measurement
Fluorescence microscopy image formation
Object intensity measurements
Global background correction
Neighborhood filters
Convolutional filters
Rank filters
Median filter
2D noisy object segmentation and filtering
Local background correction
Object filtering
Distance transform
Watershed
Nuclei and cells segmentation
Skeletonization
Similarity transformations
Running a script
Coding with LLMs
Recording a script
Variables
Strings and paths
Output saving
Functions
Loops
Batch processing
Batch exploration of segmentation results
Handling input parameters
Setting up a scripting environment
Deep learning instance segmentation
Manual segmentation
Segment Golgi objects per cell
Module overview
Extras
Reference
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