One of my many joys is photo-microscopy, where images are taken of item(s) so small that often the detail cannot be seen with the naked eye. One of it's disadvantages (as also occurs with macro-photography) is the extremely shallow depth of field. Because the optics in photo-micrography are slightly different, it is not a case of increasing the aperture but rather employing a technique known as focus stacking.
Focus stacking involves taking a number of images; each where a different part of the image is in focus and stitching them into one image with a greater level of focus. I use two tools to achieve this, one is known as Helicon Focus, and the other Helicon Remote.
Helicon remote, as the name implies is a ‘remote control' software which is designed to integrate with a compatible digital camera and a focus controller (e.g. trinamic or stackshot) which can be used to move either the microscope focus, or the camera. Within the software the various parameters are set (e.g. starting point, finishing point, number of shots) and once configured the software can automate the process of capturing a significant number of images. The software (using the camera settings you supply) captures an image, moves the motor (to move the camera or microscope focus) and captures another image, repeating the process until all images are captured.
Helicon focus is the brains behind the operation, and can operate without Helicon remote (if needed). Helicon focus is responsible for taking the images you select, and pulling out the relevant information to be focus stacked into one composite image. There are a number of different stacking options (e.g. average, depth map) but essentially the software runs through each of the images, and using an algorithm it extracts the ‘in-focus' sections of each image, and stacks them into a combined composite image. At the end this image can be tweaked (e.g. if some area's need to be excluded) and can finally be saved.
One cool feature is the depth map, which attempts to extract some depth information from the image based on the focus, and the ‘stacking'.
I have been very impressed with the support, the team have worked with me fairly quickly when I have had issues which needed resolving.