Hands-on exercises for learning Imaris
Imaris, Visualization, spots segmentation, surfaces segmentation, colocalization, spots tracking, Batch, plotting graphs with Vantage.
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.
Introduction to ImarisXT using MATLAB
Imaris scripting using Matlab (ImarisXT API trining). Slides, protocols, some scripts. Hands-on
Deconstructing co-localisation workflows: from co-expression assessment to super-resolved co-distribution analysis
Deconstructing co-localisation workflows: from co-expression assessment to super-resolved co-distribution analysis
Lecture slides
Introduction to Image Segmentation
ImageJ, GUI training for beginners. segmentation intro, thresholding, morphological segmentation
EB1 tracking with Matlab
This module follow EB1 tracking with IJ. In this session, we will visualize the tracking results and also cover typical analysis protocols for the quantitative analysis of movement. Two dynamic numerical features could be extracted from tracking results: speed and direction. Estimation of movement speed from multiple trajectories is a popular indicator of movement, and we will quickly go over the method for estimating the average speed of EB1 movement along microtubule. Movement direction is another quantitative feature, but is rarely explored.