FIJI Macro

FIJI: Macro writing for Biologists workshop

The FIJI Macro writing for Biologists workshop runs over two half-days, with follow up sessions to assist you with completing your own code. To get the most out of this workshop, you should have your own images and an image analysis workflow that you want to implement.

Day 1 (1-5pm, 25th June): We will provide introduction to the syntax of ImageJ macro language and practice basic tools (e.g. loops, condition, array). This is suitable for biologist with no previous coding knowledge. If you are coding often, you can attend day2 only, but make sure to browse the day1 material beforehand!

Day 2 (1-5pm, 27th June): We will go through few examples of image analysis workflows. Using these as templates, you can start to write your own macro using your own image (submitted during registration). You are NOT expected to complete your script on this day but continue to work at your own pace after this session.

Follow up sessions: Individuals will be able to book in a 1:1 consulting session on the 5th or 12th July (1-2 weeks after).

Ahead of registering for the event (link at the bottom of this page) please do the following:

1. Workflow

Please describe your image analysis workflow and save as a text/word file. This will be used to create your own macro

For example:

  1. Open image, split channel
  2. On Red channel, detect red positive cell
  3. On Green channel, detect green positive cell
  4. Detect cell that are positive to both
  5. Output: log cell counts to table
  6. Output: draw detected cell on the image

2. Image data

Please upload the below for use in the workshop (see instructions below)

a) A text file containing your image analysis workflow

b) Sample image(s) to use during workshop. If you are wanting to establish a batch analyses, then we will require at least 2 images.

Instructions: Go to

Type password: BOMPmacro2019!

Make your own name folder and upload a sample image (at least two images for batch analyses). Please Limit file size to 100MB