Tool installation Digital image basics Lookup tables Multichannel images Spatial calibration N-dimensional images Data types Image file formats Workflow: Quantitative image inspection and presentation Volume slicing Projections Volume rendering Segmentation Thresholding segmentation and binarization Automatic thresholding (histogram-based) Connected component labeling label mask and instance segmentation Object shape measurements Workflow: Nuclei segmentation and shape measurement Fluorescence microscopy image formation image formation Object intensity measurements Global background correction Neighborhood filters Median filter Workflow: 2D noisy object segmentation and filtering Morphological filters Rank filters, Dilation, Erosion, and Opening Local background correction Object filtering Distance transform Watershed Workflow: Nuclei and cells segmentation Skeletonization segmentation and binarization Draft: Similarity transformations OME-Zarr format Scripting: Running a script Draft: Coding with LLMs Scripting: Recording a script Scripting: Variables Scripting: Working with strings Scripting: Output saving Scripting: Batch processing Scripting: Handling script parameters Draft: Commenting Draft: Setting up a scripting environment Draft: Functions Draft: Loops Draft: Correlative image rendering visualisation Draft: Deep learning instance segmentation Draft: Manual segmentation Draft: Segment Golgi objects per cell Draft: Big image data file formats chunking and multi-scale
