Image Analysis: Basic Procedures for Description of Plant Structures - Plant Cell Morphogenesis: Methods and Protocols - page 73

Fig. 3 Analysis of epidermis—estimation of stomatal density and analysis of epidermal cell shape: ( a ) Original
image of epidermis acquired by fl uorescence microscope. ( b ) Red channel separated from the original image
(Menu/Image/Color/Split Channels). ( c ) Sampling window superimposed on the image. Three stomata are man-
ually selected, because they are lying at least partly in the frame and are not intersected by the (full-drawn)
exclusion line. ( d ) Sampling window superimposed on the adjusted image. Cells number 5, 12, 16-20, 22, 24,
26-28, 30 and 32 are selected, because they do not intersect the frame rectangle (or are inside the rectangle)
and simultaneously do not intersect the exclusion lines. Results for each cell appear in the Results table
3. If your image is a multichannel image, split the channels
(Image/Color/Split Channels) and for further analysis choose
the most contrasting channel.
4. Smooth the image (Process/Smooth).
5. Enhance the contrast (Process/Enhance contrast).
6. Set the threshold (Image/Adjust/Threshold).
7. Dilate the image (Menu/Process/Binary/Dilate).
8. If needed, edit the image manually with the pencil or paint
brush tool (More Tools/Drawing Tools).