Contents

MATLAB, for advanced analysts. Slides, Scripts, Reproduction of results & deconstruction. Uniquely designed analtical approaches towards understanding cell cluster movements, based on stress / cell migration analysis.

Fiji plugin for detecting, tracking and quantifying filopodia

ImageJ & R, for advanced analysts. Slides, Scripts, Reproduction of results & deconstruction. Segmentation of filopodia (thin filamentous structure) and analysis of their shape and movements to characterize phenotypes.

MATLAB, CellProfiler, Advanced Cell Classifier, for advanced analysts. Slides, Scripts, Reproduction of results & deconstruction. We aim to implement an image-based analysis of a biological system by profiling the phenotipic response of a cancer cell line following perturbation with a small-molecule compound library

ImageJ, for those with GUI knowledge but without scripting knowledge

ImageJ, for those with GUI knowledge but without scripting knowledge

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)

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.

In this session we will use a 3D multichannel reconstruction of zebrafish larva to explore the visualization capabilities of Matlab. We will start from extracting and inspecting single slices and will continue with combining multiple channels, finally generating a surface rendering for visual colocalization analysis.During the process we will review methods for manipulating multidimensional arrays, including resizing, reshaping and conditional selection.

This session will focus on the exploration of MATLAB functions and methodologies for image processing. We will cover aspects like importing images and metadata, as well as saving processed images and csv data files. Techniques such as image filtering, segmentation and morphological operations will be addressed. To promote a comparison with ImageJ, a simple workflow for object counting and properties extraction will be coded, using as input data the Embryos sample image.

Matlab is a commercial software for numerical computing and statistical analysis that can be used to process and analyze multidimensional images. Within this session you will get familiar with the Matlab environment and its programming language. Among the topics addressed: matrix manipulation and advanced indexing, access to files, data inspection and basic plotting. This session will provide you the foundations that you need for the following modules, where you will manipulate images, extract measurements, and statistically analyze and visualize results.

ImageJ, for those with GUI knowledge but without scripting knowledge. 

ImageJ, for those with GUI knowledge but without scripting knowledge

ImageJ, for those with GUI knowledge but without scripting knowledge, workflow: MIP, change LUT, merge channels

ImageJ, for those with GUI knowledge but without scripting knowledge, workflow: MIP, change LUT, merge channels

ImageJ, for those with GUI knowledge but without scripting knowledge, workflow: change LUT, make montage

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.

Aim: Students acquire ImageJ macro programming technique to ease
their work loads with image processing / analysis.