To get started, you can take a look at some example pipelines and other kind of examples:
Alveolar macrophages were confronted with various species of fungi, including Aspergillus fumigatus and various Lichtheimia species, followed either directly by microscopy, or first by tissue fixation and fluorescence labeling, and then confocal microscopy.
Bacterial growth measured in fluid droplets
Microfluidic droplets of approximately 100 micrometer diameter were filled with a solution containing E. coli bacteria and the bacterial growth was observed via brightfield transmitted light microscopy. This JIPipe workflow finds the droplets that show bacterial growth.
Kidney status check via glomeruli counting
This pipeline analyzes light-sheet fluorescence microscopy of whole murine kidney data. These images were generated with staining specific to glomeruli, functional units of kidney. Here, we reduced the size of the image stack from 700 to 20, which non-workstation computers can process without issues.
Nanoparticle delivery analysis in liver
Micelle nanocarriers were injected into the circulatory system of the mouse vie the tail veins. Two-photon microscopy was utilized to image the cargo delivered by the micelles to the hepatocytes, sinusoids, canaliculi and liver-sinusoidal endothelial cells.
Track analysis of unlabeled nematodes
Live worms of the species C. elegans were recorded via transmitted light microscopy. The resulting time-series images are analyzed by a JIPipe pipeline.