Diatoms of North AmericaImageJ is a free, powerful software program. It has a handy tool for measuring diatoms from light micrographs or scanning electron micrographs. At least one of your digital images needs to have an embedded scale bar.
Step 1. Open your .jpeg or .png diatom image in the ImageJ program. Be sure that it has a scale bar. We usually use 10 µm scale bars for LM images.
Step 2. Use the line tool to measure the length of the embedded scale bar. (The thin yellow line is to the left of the scale bar in the image to the right).
Step 3. Select Analyze > Set Scale from the menu. A small window will appear. Note that the length of the scale bar (in pixels) will appear. For this image, there are 244 pixels for 10 µm. I entered the known distance as "10" and the units as "micro" (I meant to write micron, oops). If you check the box for "Global", the calibration will apply to all your images.
Step 4. Now you can measure the length and width of your diatom using the line tool.
Step 5. This step is where things get cool. You can measure the number of stria density of your diatom. First, note that I drew a line starting at the central area, parallel to the apical axis. It is important to measure striae in this location! Also note that I carefully drew a line that was 5 µm long. Now, go to the menu and select Analyze > Plot Profile. The plot window shows the pattern of light and dark that my yellow 5 µm line crosses. I can count the bright peaks to find that there are 5.5 striae in 5 µm, or 11 striae in 10 µm.
Cool, right?
Step 6. Download this image by dragging it to your desktop. Find out if you get the same results when you measure it in ImageJ.
