Image Title Category Type Description Updated
Analysis of Microtubule Orientation: Tracking with ImageJ, Directionality Analysis with Matlab Training Material

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.

04/08/2019 - 14:07
Visualization of 3D images with Matlab Training Material

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.

04/08/2019 - 14:01
2D image processing and Data analysis with Matlab Training Material

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.

04/08/2019 - 13:58
Introduction to Matlab Training Material

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.

04/08/2019 - 13:52
From workflows to simple batch macros: Quantify intensity at the nuclear envelope. Training Material

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

04/08/2019 - 13:45
From workflows to simple batch macros: Measure Phalloidin in the nucleus area. Training Material

ImageJ, for those with GUI knowledge but without scripting knowledge

04/08/2019 - 13:42
Recording simple macros for batch processing v2 Training Material

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

04/08/2019 - 13:39
Recording simple macros for batch processing Training Material

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

04/08/2019 - 13:36
Batch ImageJ macro Training Material

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

04/08/2019 - 13:34
Tumor Blood Vessels: 3D Tubular Network Analysis Training Material

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.

04/08/2019 - 13:30
Macro Programming in ImageJ Training Material

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

04/08/2019 - 13:24
Hands-on exercises for learning Imaris Training Material

Imaris, Visualization, spots segmentation, surfaces segmentation, colocalization, spots tracking, Batch, plotting graphs with Vantage.

04/08/2019 - 13:20
Building a workflow with CellProfiler Training Material

CellProfiler, Counting PLA dots, track swelling organoids

04/08/2019 - 13:16
KNIME Workflow Training Material

KNIME workflow construction hands-on, example workflows in the linked materials

04/08/2019 - 13:13
ICY Protocols and Scripts Training Material

ICY workflow construction hands-on. Slides

04/08/2019 - 13:11
Introduction to ImarisXT using MATLAB Training Material

Imaris scripting using Matlab (ImarisXT API trining). Slides, protocols, some scripts. Hands-on

04/08/2019 - 13:07
ImageJ2 Ops Scripting Training Material

ImageJ2 API training. Beaker notebooks, with backends under dot-folder. Hands-on

04/08/2019 - 13:04
Developing for ImageJ and Friends Training Material

ImageJ, example IDE setup for developing plugin. Lecture and demonstration

04/08/2019 - 13:00
Big Data & 3D Visualization Training Material

Lecture Slides

04/08/2019 - 12:43
Deconstructing co-localisation workflows: from co-expression assessment to super-resolved co-distribution analysis Training Material

Deconstructing co-localisation workflows: from co-expression assessment to super-resolved co-distribution analysis

Lecture slides

04/08/2019 - 12:40