Core Biotechnology Services

Workshops

Introduction to ImageJ/Fiji and Writing macros in ImageJ

  • Monday 23 and Tuesday 24 January
  • Place - College Court
  • Organizer - Dr K.R. Straatman
  • Registration deadline - End of day Sunday 15 January

ImageJ is a public domain image processing and analysis program 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 iJust ImageJ) is a distribution of ImageJ focused on 3D image reconstruction and analysis. For the workshop I would advise to install Fiji, as some things are easier to do in Fiji, but you can use plain ImageJ as well.

Registration forms

Who should attend?

ImageJ-Fiji overview of menus, graphs and windows

The workshops are focused on anyone (scientist and non-scientists) who want to use ImageJ/Fiji for image analysis. The workshops are open to internal and external participants, including industry and business participants, who want to use or have started to use ImageJ for image analysis but need a little help to make best use of the software. During the workshops you will get an introduction into the use of ImageJ/Fiji for digital image processing focused mostly 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 23 January

A one day introduction workshop for ImageJ/Fiji. The aim of this day is to familiarize you with the use of the ImageJ/Fiji menus, plugins and macros for digital image processing and where to find information about its 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 24 January

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. So, 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 noon Monday 16 January. By cancellation after this deadline a charge of £50/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:

  • En-suite standard room: £45 + VAT per room, per night
  • Suite or Executive room: £60 + VAT per room, per night
  • Double occupancy in either of the above room types is an additional £15.00 + VAT per room, per night

Please download the College Court Bed and Breakfast Booking Form if you want to make use of this option and email the filled in form to conferences@le.ac.uk.

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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