1.      Overview: Scanner Selection and Use 

In this method, the scanning and the image analysis happen as two separate steps. A flatbed scanner is the tool of choice here to gather the digital images. Using a flatbed scanner in place of a microscope gives the combination of high resolution, large sample area, and the ability to capture multiple collector images in 1 setup, saving time. Up to 9600 DPI optical scanners are available, and at first glance it would be attractive to scan at 9600 DPI, yielding a pixel size of 2.7 microns. However in practicality, a 2 centimeter square scan at 9600 DPI becomes a file of over 2 gigabytes, and each scan can take up to 20 minutes to collect.  4800 DPI scans of 2 centimeters square yield a much more manageable 40-50 megabyte image with a pixel size of 5.3 microns. If you want to experiment with 9600 DPI, by all means do. ImageJ will process the images and all the procedures listed here will still apply. Note that you may want to use smaller sample areas, and even so you will need a sizable amount of RAM in your computer to process the images.

• Resolution: Scan at a minimum of 4800 x 4800 OPTICAL resolution in at least 24 bit color (RGB or HSB are minimum 24 bit). Some scanners use software interpolation to create a finer resolution than they are mechanically able to. Avoid interpolated resolutions. 
• Scan multiple areas: The software should be able to define and scan multiple areas in one pass and save each area to a discrete file. This will save a lot of time compared to scanning individual images. High resolution scans take time. Fourteen or more samples may be loaded in a flatbed at one time and processed in the background, freeing the technician to perform other tasks. 
• Save to an uncompressed format: The scanner software should be able to output to either .BMP format or uncompressed TIFF (preferred format for ImageJ). 
• LED instant-on light source: Consistent light is important to consistent images. Avoid scanners that require a warm-up time.