Examples
Here you can find all example projects and results. If you do not know what to do with the packages, please read through the tutorials referenced below.
👉 Tutorial: How to load projects
Please take a look at this tutorial if you don't know what to do with downloaded example projects.
👉 Tutorial: How to browse results
Please take a look at this tutorial if you don't know what to do with downloaded project + data packages.
👉 Tutorial: How to import node templates
Please take a look at this tutorial if you don't know what to do if a package comes with a Template.json file (Project + Data + Node templates).
Using the Coloc2 nodes
A small example showcasing how to utilize the Coloc2 nodes.
Host-pathogen interactions
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.
Conversion between ROIs and labels
A small example showcasing nodes for conversion between labels and ROIs and vice versa.
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.
Training of a fully automated pipeline for detecting tissue in MSOT data
For our 'MSOT cluster analysis toolkit' (MCAT), we developed a deep-learning-based approach for detecting the mouse tissue. The training was applied in JIPipe via our Cellpose nodes.
Using the Omnipose segmentation nodes
A small example showcasing how to utilize the Omnipose nodes.
Using the Analyze skeleton 2D/3D
A small example showcasing how to utilize the Analyze skeleton 2D/3D node.
Using the TrackMate nodes
A small example showcasing how to utilize the TrackMate nodes.
Tutorial: Adding and running nodes
Accompanying data and project for the tutorial 'Adding and running nodes'.
Tutorial: Importing an image I/II/III
Accompanying data and project for the tutorial series 'Importing an image'.
Tutorial: Importing a directory of images I
Accompanying data and project for the tutorial 'Importing a directory of images I'.
Tutorial: Importing a directory of images II
Accompanying data and project for the tutorial 'Importing a directory of images II'.
Tutorial: Handling multi-channel images I
Accompanying data and project for the tutorial 'Handling multi-channel images I'.
Tutorial: Creating node groups
Accompanying data and project for the tutorial 'Creating node groups I/II'.
Tutorial: Creating node templates
Accompanying data and project for the tutorial 'Creating node templates'.
Tutorial: Annotations I (Filtering)
Accompanying data and project for the tutorial 'Annotations I: Filtering'.
Tutorial: Annotations II (Branching)
Accompanying data and project for the tutorial 'Annotations II: Branching'.
Tutorial: Annotations III (Modifying and merging)
Accompanying data and project for the tutorial 'Annotations III: Modifying and merging'.
Tutorial: Compartments I (Creating and connecting)
Accompanying data and project for the tutorial 'Compartments I: Creating and connecting'.
Tutorial: Quantification and plotting
Accompanying data and project for the tutorial 'Quantification and plotting'.
Tutorial: Cache I (Generating and viewing)
Accompanying data and project for the tutorial 'Cache I: Generating and viewing'.
Tutorial: ROI processing
Accompanying data and project for the tutorial 'ROI processing'.
Tutorial: Image properties and LUT
Accompanying data and project for the tutorial 'Image properties and LUT'.
Tutorial: Table processing
Accompanying data and project for the tutorial 'Table processing'.
Tutorial: Exporting data I (Machine-readable)
Accompanying data and project for the tutorial 'Exporting data I: Machine-readable'.
Tutorial: Exporting data II (Human-readable)
Accompanying data and project for the tutorial 'Exporting data II: Human-readable'.
Tutorial: Annotating data with measurements
Accompanying data and project for the tutorial 'Annotating data with measurements'.
Tutorial: Multiple parameter sets
Accompanying data and project for the tutorial 'Multiple parameter sets'.
Tutorial: ImageJ macros
Accompanying data and project for the tutorial 'ImageJ macros'.
Tutorial: Loops
Accompanying data and project for the tutorial 'Loops'.
Tutorial: Python
Accompanying data and project for the tutorial 'Python'.
Tutorial: Cellpose I (Segmentation)
Accompanying data and project for the tutorial 'Cellpose I: Segmentation'.
Tutorial: Cellpose II (Training)
Accompanying data and project for the tutorial 'Cellpose II: Training'.
Using the Weka segmentation nodes
A small example showcasing how to utilize the Trainable Weka Segmentation nodes.
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.