Introduction To Image Analysis

7 Dec 2020, 09:00 → 9 Dec 2020, 17:30 Europe/Berlin

Helene Hoffmann, Steve Schmerler (HZDR)

Description

The course introduces novice users to basic concepts and techniques in quantitative image analysis.  Major topics covered include image characteristics and visualization, object detection, image segmentation and extraction of quantitative measurements. Participants will learn how to automate their analysis with ImageJ macros.
The course will be a combination of presentations, interactive demos and numerous hands-on exercises. For hands-on sessions we will be using Fiji and Ilastik.

The entire course will be held online with zoom. So if you want to participate, make sure that you have zoom installed and a stable internet connection as well as a microphone and speakers/headphones.

The course will be a combination of presentations by the instructors, live demos and hands-on sessions. The software used for the practical sessions will be Fiji which is available free of charge.

The course is free of charge and provided as an in-kind contribution of FWCC.

 

Presenters

• Noreen Walker <walker@scionics.de>
• Gayathri Nadar <nadar@scionics.de>

If you have questions regarding the course content, please concact them. They also manage the zoom room.

 

Time and Location

 

• When: 7. - 9. November 2020, 09:00 - 17:30 CEST
• Where: Online via Zoom (the link will be shared with all participants by email 1-2 days before the course)
• Language: English

Shared Document

We use a shared document to keep our collaborative notes. You can find it here.

Course Content

Here are the topics covered in the course:

• Image basics, Visualization, Measurements, Counting objects
• Segmentation (1): classic segmentation pipeline
• Image Filters, Morphological Operations
• Segmentation (2): pixel classification (trainable segmentation)
• [ 3D Data: Basics and Visualization]
• Good practices
• ImageJ Macro Basics
• Batch processing with macros

Registration and Check-In Task

The registration is closed.

You do not need to set up an Indico account to register. The registration button can be found at the bottom of the description during the registration period.

After registration please complete the following check-in task:

• Set up the required tools for the workshop (see section Requirements below).

We currently only have 20 seats available in the course, that are provided on a first-come-first-serve basis.

Requirements

Installing Fiji and Ilastik:

Please see the installation guide attached at the end of the page.

Other prerequisites:

• Computer, preferably with external monitor (not required)
• Mouse (a touchpad is not enough)
• Zoom installation

Course material:

• The download link for the material (image data) will be made available before the course.

Related online material

• Robert Haase: Lecture BioImage Analysis (Dresden)
• NEUBIAS Academy @Home
• EPFL: image processing and analysis for life scientists

instructions_software_setup.pdf

Monday 7 December

1 Image basics, Visualization, Measurements, Counting obejcts

12:30 Lunch break

2 Segmentation(1): classig segmentation pipeline

Tuesday 8 December

3 Image Filters, Morphological Operations; Segmentation (2): pixel classification (trainable segmentation)

12:30 Lunch break

4 Segmentation (2): continued; [ 3D Data: Basics and Visualization]; Good practices

Wednesday 9 December

5 ImageJ Macro Basics

12:30 Lunch break

6 Batch processing with macros