Micrographia@Western is excited to be offering a short 3-afternoon course on microscope image analysis. These afternoon tutorials, running June 23, 24, & 25, will teach you three core skills needed to perform several common image analysis tasks – basic quantification, colocalization, and image segmentation using AI.
Each session is a stand-alone session, so you can pick and choose which sessions you attend. All three sessions are free, but space is limited, so you must sign up for each session you wish to attend. Prior to each session you will need to install some software and download some datasets – videos will be provided to assist you with this. There are no other pre-requisite, but to get the most out of them you will need to bring a laptop to each session, and you will need to install some free software prior to the sessions. A short description of each day’s module, and signup links, can be found below.
Note: space is limited and registration is based on a first-come, first-served basis.
Images are full of spatial, intensity, structural, and other data – but proper techniques are required to extract this information from your images.
Filtering of chloroplasts to remove background and prepare for quantificaiton
In this session we will go over the most common image analysis tasks in the free and open-source image analysis package FIJI. This includes opening and manipulating images, image filtering, basic image adjustments, intensity measurements, thresholding, and basic binary operations.
Date: Tuesday June 23, 1-4 PM
Software Needed:
- FIJI – a free and open-source image analysis package that is expandable via a large library of plug-ins.
Video Tutorial for Software/Plugin Instillation: Installing FIJI
Day 1: Image Analysis
Micrographs can be used to detect the co-expression of proteins in cells, the accumulation of markers on the same subcellular structures, and even test for the presence of inter-protein or inter-object interactions. The techniques for quantifying these forms of interaction are collectively known as colocalization, and when used properly, can be a powerful analytical tool.
Pearson’s colocalization analysis (right) of the interaction between microtubules (magenta) and actin (yellow) in epithelial cells (left).
In this session we will discuss several colocalization metrics, their use, and their interpretation. You will learn how to employ these methods in a statistically robust fashion. Each method will be applied in a series of hands-on exercises using the JACoP colocalization tool in ImageJ.
Date: Wednesday June 24, 1-4 PM
Software Needed:
- ImageJ or FIJI – these are two variants of the same free image analysis software programs. It may be simpler to use ImageJ, but FIJI has greater capabilities.
- Just Another Colocalization Plugin (JACoP) – this is an excellent colocalization plugin for ImageJ/FIJI and it has an accompanying paper to help you understand each analysis.
Video Tutorial for Software/Plugin Instillation: Installing FIJI and Just Another Colocalization Plugin
Day 2: Colocalization
One of the most common goals in image analysis is to identify and separate different objects in an image based on characteristics such as brightness, shape, size, and texture. Historically, this was a difficult process that often required human annotation. New trainable machine learning algorithms have revolutionized automated segmentation.
Segmentation of macrophages (circled) from collagen autofluorescence in heart tissue stained with anti-CD68.
In this session we will dive into approaches to segmentation using new and emerging machine learning and pre-trained AI tools. These tools greatly simplify this otherwise complex task. We will finish this session with a hands-on tutorial in Ilastik, where we will segment and classify some difficult images.
Date: Thursday June 25, 1-4 PM
Software Needed:
- Ilastik – a free and open source machine learning tool for segmentation and other pixel classification tasks.
- FIJI – a free image processing software package
Video Tutorial for Software/Plugin Instillation: Installing ilastik and Linking it to FIJI