Aim: What is ImageJ and Why do we use it?

Day 1

Brief Background

• Released in 1997 by Wayne Rasband

• Developed at the National Institutes of Health

• Runs on Windows, Mac, and Linux

• Macros enable personalization and allows for focus on specific tasks

Background• FREE!! Runs on Java with

no license required– Predecessors such as

Image SXM and NIH Image were “closed source” …requires fee/license

• More than 1700 users on the mailing list– Countless others use for

independent research

Why do we need to learn about it?

• Increase technical computer skills

• More accurate than hand calculations or guess-timations

• Allows you to manipulate data

Ok, so what is it?

• Long answer: a public domain, Java-based image processing program • Short answer: pixel analysis

How to use ImageJ (The basics)

• Go to My Website (Mrs. Farley) through the Elmont web page

• Right-click to open ImageJ in a new tab– If you are working at home, download the

program so you can avoid step 1.• If you have images saved, use those.– If not, right click sample files and save them to

desktop or another folder

How to set Scales

• File– Open– Select image

• Go back to ImageJ toolbar

• Straight Line Selections

• Click to start line on scale

• Click to stop line on scale

How to set scales

• Analyze• Set Scale• Change known

distance to units on scale in picture

• Change unit of length to units provided (km,m,mm,um, etc.)

• Click global• Click OK

How to measure length

• Use straight line tool• Draw line on selected

area• Analyze• Measure• Scroll to the right of

data table • Find length; record

How to measure length with a non-straight line

Segmented Line• Right click the straight line

tool• Select segmented line• Click repeatedly to match

line shape to original image• Analyze is the same

Free-Hand • Right click the straight line

tool• Select freehand• Click and drag• Analyze is the same• **NOT RECOMMENDED**

Assignment

• Junior High Researchers– Analyze images B, C, and D for distance of one side

and total perimeter • Senior High Researchers– Analyze images A-E for “height”, “Width” and total

perimeter• Email data to your teachers today (Mr.

Spinnato or Mrs. Flannory)