Basic Introduction Into Optics & Microscopy - Lecture - JSC2025

A lecture given by Dr. Zoltán Cseresnyés that gives a basic introduction into optics and microscopy in the context of microbiology. Please note that we experienced issues with the audio recording.

Basic Introduction Into Bioimage Analysis - Lecture - JSC2025

A lecture given by Dr. Ruman Gerst that gives a basic introduction into image analysis and establishes a toolbox of commonly used image processing methods. Please note that we experienced issues with the audio recording.

JIPipe Tutorial (2025) - Basic Setup - JSC2025

Explains the download and initial setup of JIPipe and gives a brief overview of the user interface.

JIPipe Tutorial (2025) - Basic Blobs Segmentation - JSC2025

Full interactive tutorial on how to use the JIPipe user interface and create a basic blobs segmentation workflow, showcasing how to import images, apply auto-thresholding, detect particles, and visualize the results.

JIPipe Tutorial (2025) - Intermediate Analysis - Kidney Tissue & Glomeruli - JSC2025

Full interactive tutorial on creating an intermediate-level analysis in JIPipe that segments and analyzes LSFM data from kidneys (Klingberg et al., 2017) involving feature detection, ROI-based filtering, and the branching pathways.

JIPipe Tutorial (2025) - Workflow Organization - Compartments - JSC2025

Full interactive tutorial on how to structure JIPipe workflows using compartments. Requires the kidney analysis workflow (follow earlier tutorial or download the workflow; see below). Also briefly showcases how to annotate graphs with text/comment boxes.

JIPipe Tutorial (2025) - Group Nodes - JSC2025

Brief tutorial on how to create and edit group nodes inside JIPipe.

JPipe Tutorial (2025) - Sharing Nodes & Projects - JSC2025

Full interactive tutorial on how to create and share node templates and how to make use of the project overview to create project-wide parameters.

JIPipe Tutorial (2025) - Batch Processing - JSC2025

Full interactive tutorial on how to convert a single-image analysis workflow into a batch processing pipeline. Requires the blob analysis and kidney analysis workflows (follow previous tutorials or download the workflows; see below). Introduction into text annotations and annotation-guided batch processing.

JIPipe Tutorial (2025) - Path Processing & Exporting Results - JSC2025

Full interactive tutorial on how to automatically export results generated from a JIPipe workflow. Introduction into basic path processing features.

JIPipe Tutorial (2025) - Expressions & Advanced Features - JSC2025

Lecture on how to use JIPipe's expression language and brief overview of other more advanced features.

JIPipe Tutorial (2025) - Workflow Showcase - Neutrophil Segmentation & Tracking - Cellpose - JSC2025

Showcase of a real-world workflow for fully automated segmentation and tracking of neutrophils in transmitted-light images. Usage of Cellpose segmentation and TrackMate 7 tracking nodes.

Homework Discussion - Microscopy - JSC2025

Recording of the microscopy homework discussion.

Homework Discussion - JIPipe - JSC2025

Recording of the JIPipe homework discussion.