Core Biotechnology Services

Workshops

Introduction to ImageJ/Fiji and Writing macros in ImageJ

  • Monday 16 December and Tuesday 17 December 2024
  • Place - College Court
  • Organizer - Dr K.R. Straatman
  • Registration deadline - End of day Sunday 8 December

ImageJ is a public domain image processing and analysis software package written in Java. It is freely available and used by many scientists around the world. There is a very active ImageJ community and ImageJ is continuously improved. Fiji (Fiji stands for Fiji is Just ImageJ) is a distribution of ImageJ focused on 3D image reconstruction and analysis. The workshop will focus on Fiji, but you can use plain ImageJ as well. The attendees will learn how to use ImageJ/Fiji to analyse features in microscope images but the used techniques are widely applicable to other types of images.

Registration forms

Who should attend?

ImageJ-Fiji overview of menus, graphs and windows

The workshops are for scientists and non-scientists who are interested in using ImageJ/Fiji for image analysis. The workshops are open to internal and external participants, including those from industry and business, who want to use or have started to use ImageJ/Fiji for image analysis but need a little help to make the best use of this software. During the workshops, you will get an introduction to the use of ImageJ/Fiji for digital image processing, but the workshops are mostly focused on biological examples. Experience with ImageJ is not required, but a basic understanding of the use of a computer/laptop is an advantage.

Please be aware, participants have to bring their own laptop!

Content and program

Introduction to ImageJ/Fiji; Monday 16 December 2024

A one day introduction workshop for ImageJ/Fiji. The aim of this day is to familiarise you with the use of the ImageJ/Fiji menus, plugins and macros for digital image processing and where to find information about their use. During this day, there will be lectures and hands-on sessions on the basics of ImageJ/Fiji and we will have a closer look at a selection of macros and plugins.

  • 9.30am - 10.30am: Introduction lecture
  • 10.30am - 11.00am: Coffee/tea
  • 11.00am - 12.30pm: Hands-on session
  • 12.30pm - 1.30pm: Lunch
  • 1.30pm - 2.30pm: Plugins lecture
  • 2.30pm - 3.30pm: Hands-on session
  • 3.30pm - 4.00pm: Coffee/tea
  • 4.00pm - 5.00pm: Hands-on session

After the workshop there will be time to discuss individual questions concerning image analysis using ImageJ/Fiji on own data.

Writing macros in ImageJ; Tuesday 17 December 2024

The second day is a workshop introducing the ImageJ macro language, which can be used for automated image analysis in imageJ/Fiji. The macro language is a powerful tool to analyse large data sets. During this workshop, we will see how to select a directory using the macro language, how to write a macro to analyse the data and how to reuse code. This means that during this workshop, you will write code using the macro language. However, programming knowledge is not required to follow the workshop.

  • 9.30am - 10.30am: Introduction to macros
  • 10.30am - 11.00am: Coffee/tea
  • 11.00am - 12.30pm: Hands-on session
  • 12.30pm - 1.30pm: Lunch
  • 1.30pm - 3.00pm: Hands-on session
  • 3.00pm - 3.30pm: Coffee/tea
  • 3.30pm - 5.00pm: Hands-on session

After the workshop there will be time to discuss individual questions concerning image analysis using ImageJ/Fiji on own data.

Workshop fees

 Workshop Academic/student fees     Industry/business fee
 Introduction to ImageJ/Fiji   £   85.00  £ 130.00
 Writing macros in ImageJ  £   85.00  £ 130.00
 Both workshops  £ 150.00  £ 240.00

Fees include lecture notes, refreshments and lunches.

Payment methods

Participants from the University of Leicester have to use an internal charge code for payments. For external participants we only accept credit card payments via shop@le for the workshop fee. Accommodation (if required) has to be organized separately (see below). Once the registration form has been submitted you will receive a link to make use of the shop. For billing purpose you will be asked to create an account with shop@le. Payment has to be received before the start of the workshop.

Cancellations

There will be a 10% cancellation fee when a cancellation is received before Monday 9th of December 2024. By cancellation after this deadline a charge of £40/day will be in place. Substitutions can be made, but please inform us in writing.

Bed and Breakfast

The workshops will be given at College Court, at walking distance from the University of Leicester and the city centre. Workshop participants can also arrange Bed and Breakfast at College Court. Please contact College Court directly for pricing. 

Quick links

The workshops are organized by Dr Kees Straatman (krs5@le.ac.uk), manager of the Advanced Imaging Facility, part of the Core Biotechnology Services from the College of Life Sciences, University of Leicester.

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