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Image Analysis I

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Image Analysis I Biology UNI 2005 What is image analysis? Start with image (digital) Cell through microscope Forest from satellite Any scale in between Determine ... – PowerPoint PPT presentation

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Title: Image Analysis I


1
Image Analysis I
  • Biology UNI
  • 2005

2
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 (marked) items
  • Counts of particles by size
  • Movement, path length

3
Why use image analysis?
  • Convenient
  • When you want
  • Where you want
  • Time not a problem
  • Capture a snapshot in time
  • Analyze it later for multiple things
  • Can learn more than every before

4
Poor mans example
  • Lines and shapes
  • From PPT
  • Connect two spots
  • Format Autoshape/Size
  • Size gives length of line
  • Make a box or oval that just covers the item you
    want to know about
  • Format Autoshape/Size
  • Size gives height, width
  • Formulas give other dimensions

5
Scaling
  • Usually want to know size of item on image, not
    screen
  • Need something in image that gives scale
  • Often a ruler or scale bar (microscopes)
  • Measure image of scale (inches, cm, pixels)
  • Measure item of interest
  • Convert item of interest to real units

6
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

100 µm
cell
7
Caution and scales
  • Scale and image of interest must be
  • Together in original image
  • Or taken at same magnification
  • At the same distance from the camera
  • Common types of scale
  • Electron microscope automatic
  • Microscope scale on stage
  • Camera ruler or meter stick in original image
  • Airplane, satellite know distances between items

8
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?
9
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?
10
Conversion help
  • Doing just a few?
  • Set up neatly on paper
  • Calculator
  • Or do in your head
  • More than three? Excel
  • Yellow cells formulas
  • Check first by hand?

100 µm
cell
11
Limitations to this method
  • Only a few types of measurement
  • Not angle
  • Not circumference
  • Not density
  • Cant handle irregular shapes, paths
  • Time to do it as the big boys and girls do

12
Image analysis programs
  • Several out there
  • Biologists favorite NIH Image/Scion Image
  • Mac/PC
  • Macs generally better for images (design)
  • PCs OK now
  • Free download
  • Google Scion Image/Download
  • Your tax dollars developed
  • Manual included, but other help not given
  • Download site run by frame grabber board company
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