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