Working with objects: measurements in 2D and 3D
ImageJ, GUI training for beginners, Count and Measure 2D nuclei,Count number of foci on 3D image , compare 2D, 2.5D, 3D results (simple workflows)
Workflow
A workflow is a set of components assembled in some specific order to
- Measure and estimate some numerical parameters of the biological system or
- Visualization
for addressing a biological question. Workflows can be a combination of components from the same or different software packages using several scripts and manual steps.
Analysis of Microtubule Orientation: Tracking with ImageJ, Directionality Analysis with Matlab
We take an example image data of microtubule binding protein EB1, and will study how to automatically track those signals and how to analyze the tracking results. We use ImageJ for measuring the temporal changes in signal positions, and will feed the tracking results for analyzing their dynamics using Matlab in the following session.
From workflows to simple batch macros: Quantify intensity at the nuclear envelope.
ImageJ, for those with GUI knowledge but without scripting knowledge.
From workflows to simple batch macros: Measure Phalloidin in the nucleus area.
ImageJ, for those with GUI knowledge but without scripting knowledge
Tumor Blood Vessels: 3D Tubular Network Analysis
In this session, we will implement a simple ImageJ macro to segment and analyze the blood vessel network of a subcutaneous tumor. The analysis is fully performed in 3D, and possible strategies to extract statistics of the network geometry and interactively visualize the results are also discussed and implemented.