Stacking & stitching


Most people who enjoy using a microscope wish, sooner or later, that they could use a camera to capture the wonderful images that the microscope provides.  Stacking and stitching photographs taken through the microscope allows a much larger area of a specimen (in some cases the whole specimen) to be photographed at magnifications useful for display or further study.

Once they have found a satisfactory way to attach a camera to their microscope, they begin to take photographs, and while these can give a great deal of pleasure, they may feel vaguely unsatisfied with some aspects of their efforts. Why might this be?

Consider how we use a microscope when we are examining a slide. It is not just our eyes that are busy, but also our hands. What are we using our hands for? Usually one hand is gently turning the fine-focus control to follow the contours of the subject and examine its depths, while the other is operating the stage controls to slowly scan across the subject.

What happens when we take a photograph? We have chosen to record just one particular focal plane within the subject, and one particular field of view across the whole breadth of the subject. This is the equivalent of the landscape photographer capturing a single patch of meadow, when a whole vista is in front of him. We would dearly like to be able to take photographs through the microscope that are a better representation of the whole of the subject we can see through the eyepieces, and thanks to digital photography and some software wizardry, we can.

Stacking allows us to combine a series of digital images of the same subject area, taken at different focal planes, into a single image with great depth of field, using a computer program.

Stitching allows us to combine a series of digital images of different parts of a subject into a panoramic view of the whole subject that retains good definition, using a computer program.

In fact by combining stacking and stitching techniques we can create our own highly detailed ‘micro-panoramas’ much like the landscape photographer standing on top of a hill and panning his camera to create a panoramic image of the view in front of him. These panoramas are potentially very large images. They can be panned around, and in the case of stacked and stitched images, zoomed into, without loss of resolution and pixellation which would occur with normal images. In consequence they can take up a lot of disk space and need to be uploaded to a hosting site if they are to be shared.

Stacking and stitching presentation

Click the arrows to move through the slides. Click the symbol at bottom right for a larger version.

Pan and zoom a stacked and stitched image

As an example of the spectacular results that can be achieved with stacking and stitching, take a look at this image of a louse from a vulture:

Stacking and stitching summary

Stacking and stitching, together and separately, can be valuable techniques to maximise the appearance and information value of photomicrographs.

Modern DSLR cameras with Live View, computer control, and perhaps now mirrorless cameras such as the Sony NEX-5N, make stacking and stitching much easier.

Very good and easy to use software is available to the amateur and has made the subject much more accessible.

David Linstead

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