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.

Using the Coloc2 nodes

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colocalization
simple
tutorial
A small example showcasing how to utilize the Coloc2 nodes.

Host-pathogen interactions

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fluorescence
confocal
cellpose
complex
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

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droplets
cellpose
complex
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

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kidney
lsfm
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

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simple
tutorial
A small example showcasing nodes for conversion between labels and ROIs and vice versa.

Nanoparticle delivery analysis in liver

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liver
published
complex
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

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msot
real data
published
cellpose
complex
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

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segmentation
deep learning
simple
tutorial
A small example showcasing how to utilize the Omnipose nodes.

Using the Analyze skeleton 2D/3D

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simple
tutorial
A small example showcasing how to utilize the Analyze skeleton 2D/3D node.

Using the TrackMate nodes

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tracking
simple
tutorial
A small example showcasing how to utilize the TrackMate nodes.

Tutorial: Adding and running nodes

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simple
tutorial
Accompanying data and project for the tutorial 'Adding and running nodes'.

Tutorial: Importing an image I/II/III

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simple
tutorial
Accompanying data and project for the tutorial series 'Importing an image'.

Tutorial: Importing a directory of images I

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simple
tutorial
Accompanying data and project for the tutorial 'Importing a directory of images I'.

Tutorial: Importing a directory of images II

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simple
tutorial
Accompanying data and project for the tutorial 'Importing a directory of images II'.

Tutorial: Handling multi-channel images I

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simple
tutorial
Accompanying data and project for the tutorial 'Handling multi-channel images I'.

Tutorial: Creating node groups

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simple
tutorial
Accompanying data and project for the tutorial 'Creating node groups I/II'.

Tutorial: Creating node templates

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simple
tutorial
Accompanying data and project for the tutorial 'Creating node templates'.

Tutorial: Annotations I (Filtering)

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simple
tutorial
Accompanying data and project for the tutorial 'Annotations I: Filtering'.

Tutorial: Annotations II (Branching)

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simple
tutorial
Accompanying data and project for the tutorial 'Annotations II: Branching'.

Tutorial: Annotations III (Modifying and merging)

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simple
tutorial
Accompanying data and project for the tutorial 'Annotations III: Modifying and merging'.

Tutorial: Compartments I (Creating and connecting)

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simple
tutorial
Accompanying data and project for the tutorial 'Compartments I: Creating and connecting'.

Tutorial: Quantification and plotting

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simple
tutorial
Accompanying data and project for the tutorial 'Quantification and plotting'.

Tutorial: Cache I (Generating and viewing)

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simple
tutorial
Accompanying data and project for the tutorial 'Cache I: Generating and viewing'.

Tutorial: ROI processing

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simple
tutorial
Accompanying data and project for the tutorial 'ROI processing'.

Tutorial: Image properties and LUT

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simple
tutorial
Accompanying data and project for the tutorial 'Image properties and LUT'.

Tutorial: Table processing

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simple
tutorial
Accompanying data and project for the tutorial 'Table processing'.

Tutorial: Exporting data I (Machine-readable)

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simple
tutorial
Accompanying data and project for the tutorial 'Exporting data I: Machine-readable'.

Tutorial: Exporting data II (Human-readable)

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simple
tutorial
Accompanying data and project for the tutorial 'Exporting data II: Human-readable'.

Tutorial: Annotating data with measurements

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simple
tutorial
Accompanying data and project for the tutorial 'Annotating data with measurements'.

Tutorial: Multiple parameter sets

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simple
tutorial
Accompanying data and project for the tutorial 'Multiple parameter sets'.

Tutorial: ImageJ macros

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simple
tutorial
Accompanying data and project for the tutorial 'ImageJ macros'.

Tutorial: Loops

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simple
tutorial
Accompanying data and project for the tutorial 'Loops'.

Tutorial: Python

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simple
tutorial
Accompanying data and project for the tutorial 'Python'.

Tutorial: Cellpose I (Segmentation)

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simple
tutorial
Accompanying data and project for the tutorial 'Cellpose I: Segmentation'.

Using the Weka segmentation nodes

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weka
simple
tutorial
A small example showcasing how to utilize the Trainable Weka Segmentation nodes.

Track analysis of unlabeled nematodes

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nematodes
real data
published
complex
Live worms of the species C. elegans were recorded via transmitted light microscopy. The resulting time-series images are analyzed by a JIPipe pipeline.