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Using ImageJ with Fibers

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					Using ImageJ to Measure Fibers   E. Stanley & M. Waterman Oakwood University HHMI Workshop
August 9, 2010       Adapted from Counting Sheep: Image Analysis by Claudia Neuhauser




Using ImageJ to Measure Fibers
ImageJ is a NIH resource for processing and analyzing images. The software can be downloaded from the
ImageJ web site: http://rsbweb.nih.gov/ij/

The documentation can be found at http://rsbweb.nih.gov/ij/docs/index.html

More tutorials are found at: http://rsbweb.nih.gov/ij/docs/examples/index.html



Learning Objectives

You will be able to

   load images into ImageJ
   prepare images for image analysis
   perform simple image analysis (counting and measuring)
   save image data to excel files

Knowledge and Skills

   using imaging software for image analysis
   mathematical concepts: scale, circularity
   measurement of length for objects



Introduction

ImageJ is a public domain software that can be downloaded on a variety of platforms, including
Windows and Mac. The software can convert many image formats including GIF, JPEG, and TIFF to to 8-
bit, 16-bit, or 32-bit images, which can then be analyzed by ImageJ.

We will use ImageJ to measure distances and count objects. Since TIFF is the least degradable format
when an image is repeatedly used for analysis, it is recommended to save any image first as TIFF before
conversion to 8-bit, 16-bit, or 32-bit.



Measuring Objects




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Using ImageJ to Measure Fibers   E. Stanley & M. Waterman Oakwood University HHMI Workshop
August 9, 2010       Adapted from Counting Sheep: Image Analysis by Claudia Neuhauser

Measuring objects and setting scale is useful in any image analysis. We will start by measuring the length
of the scale bar in a micrograph. Load the image fibers.jpg




Use the straight line tool (5 squares in from the left) in the toolbar to measure the scale bar in the
bottom right. Once a straight line is drawn, choose Analyze from the menu bar and click on Measure.
Now select Set Scale and enter the Known Distance as 45 and then the Unit of Length as microns. Click
on Global and OK to record further measurements.

Use the straight line tool to determine the length of each of the fibers. You will need to Measure each
for the record to appear in the results table. Save this table so the lengths will be saved in an Excel file.




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