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