Image Analysis with ImageJ Plant Physiology 2008 UNI

What is image analysis? Start with image (digital) –Cell through microscope –Forest from satellite –Any scale in between Determine properties of image –Dimensions –Color –Presence of tagged items –Counts of particles by size –Movement, path length

Why use image analysis? Convenient –When you want –Where you want Time not a problem –Capture a “snapshot” in time –Analyze it for multiple things Can learn more than every before

What is cell diameter? 100 µm bar is –Right click/Format/Size –3” on screen –3” = 100 µm –1” = 33.3 µm (get this form) Cell is 2” on screen –Right click/Format/Size 2” x 33.3 µm/” = 66.6 µm cell 100 µm

Examples to try #1 How tall is the tree from its visible base (pretend it is on the sled)? Dad is 6’ tall. What is the problem with measuring house height here from 6’ tall George?

Examples to try #2 How far apart are these two nucleoli (center to center)? Scale bar is 65 µm. The peak on the right is 1250 m higher than the one on the left, and they are at equal distance from the camera. How far apart (as the crow flies) are the summits?

ImageJ Program made with your tax dollars Free download (ImageJ download on Google) so you can use it at home Developed for cell biology at NIH Used at all scales now

Getting started Open program (desktop or Start/programs) File/…choose your file

Set the Scale Click on the line tool Draw a line of known length on ruler (etc.) Analyze/Set Scale Put length of line in “Known Distance” Check that units are right OK

Measuring a straight distance Pick line tool Make line on image Analyze/Measure Results box appears –Wait for numbers –Length is on far right (scroll) Make next line, Analyze/Measure Keep going

Measuring a segmented line OK for curves, irregular lines Line tool/Right click/Segmented line To draw line –Click to start –Click at next point –Continue to click at points along the way –Double click to end line Analyze/Measure

Measuring an Angle Angle tool Draw your angle –Click at one end of one arm of angle –Click at vertex –Click at end of other arm of angle Analyze/Measure Read the results

Other things you can measure Areas (rectangles, irregular shapes) Circumferences Many more Course manual has specifics

The tools

Saving results Keep track of which measurement is what Each new tool gets a new results box You will be asked if you want to save the box –Always “Results.xls”….name it something else –Otherwise one will copy over the last –Make name descriptive

Labels? Better to do these in PowerPoint