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Please notice that this article series was started in 2002!
Back then digital cameras were few and far between, and film cameras, macrom lenses and scanning your flies in a flat bed scanner was the order of the day.
Today most people have a digital camera (or even a phone), which can do decent macro shots, and much of what you can read here is very out of date. But the general methods and advice still holds, and the articles should still be worth reading.
GFF's Guide to Digitizing Flies
From Feathers to Bits

By Martin Joergensen (supported by Steve Schweitzer)

Many tiers want to get pictures of their flies into the computer for web, application or print use or just to have as a nice wallpaper or screen saver. Here's how you do.

Selecting a scanner
Flatbed scanner
 
Author Martin Joergensen's flatbed and slide scanner
The flatbed scanner (left) is definitely the best choice if you want a universal scanner. Buying a slide scanner can be a good second choice if you have lots of slides or want to handle negatives.
 
The easiest scanner to use and least expensive to buy is a flatbed scanner. These have fallen drastically in price and the quality is better than ever. Get a letter size or A4 scanner. The quality of the absolutely cheapest ones reflects the price, but rising just above the level of cheap will bring you into the amazing quality of the lower middle class. These scanners have an optical resolution between 300 and 1200 dots per inch (dpi). Aim for at least 600 dpi both vertically and horizontally. Ignore all praises that say 3600 dpi or even 4800. This is a purely software based resolution, which is created from the same optical results as any 600 or 1200 dpi scanner can produce. Your picture will not get better by increasing the resolution beyond the optical resolution - just larger.
Go for brand names and make sure that you get good software. The best software is usually light versions of the bigger and well-known applications or serious, tailor made applications. Do not content yourself with so-called user friendly, easy-to-use programs with naive, colorful user interfaces and lack of manual controls. You need to be able to manipulate all aspects of the scanned pictures to get the best results. See "GFF's Guide to Digital Picture Afterwork" for more information on the demands on the program.
You must also reassure yourself that the scanner has a plug-in or Twain module, which enables it to be used from literally any photo editing program.

Slides and negatives
Slide scanners or scanners with transparency adapters can scan slides and film negatives. Both types of originals are usually better than prints, which as a rule of thumb always will contain more contrast and less tonal richness.
Most slide scanners have configurations for both positives and negatives, and it is important to choose the right settings. Scanning negatives in slide mode and then inverting the pictures is not adequate.
True 35 millimeter slide scanners are still rare, but falling in price. Many flat bed scanners can be equipped with a slide unit, but these will not enable the scanner to scan the common 35mm slides in a proper quality. The basic resolution is not good enough. If you want to scan 35mm negatives or slides, we recommend that you buy a dedicated slide scanner. It will add to the equipment bill, but the result is pro quality scans.

The scanning process
Scanning prints
The most straightforward way is to scan a good photo of the fly. You can learn how to get good pictures of flies by reading the "GFF's Guide to Photographing Flies". The common flat bed scanners can take any common size print.
Scanning is an art onto itself, and much can be done in the scanning and following process, but one rule is of utmost importance: always have the best raw materials. Photos should be:
  - properly exposed
  - sharp - also in the depth
  - with proper light and contrast
  - well composed
When you scan, make sure that you use the optimum settings in your scanner program. Many programs have automatic exposure, which is worth trying first. Often it is needed with some manual fiddling - especially if you are working with pictures, which are beyond the average. See "GFF's Guide to Digital Picture Afterwork" for more information on this process.

Scanning flies
If you have a flat bed scanner, you actually already have an excellent large format digital camera. In this case you should certainly try scanning flies directly in the scanner. The results can be amazing. And it is the fastest and easiest way to get your flies into the computer.
The method has its limitations. It is quite difficult to do anything artsy and the three-dimensional effect is limited. You can practically only depict the fly from the side and large, round flies or flies with very large, stiff hackles can be difficult to catch properly on the picture. The depth of the picture is also limited, so backgrounds, as you know it from real pictures taken with a camera, are usually not an option.
But there are a few ways that you can make your scanned flies look good.

Keeping the flies in shape with a frame
This is an example of a home-made scannerbed fly frame.  It is about 3/8" thick and prevents the scanner lid from smashing a small 3D object like a fly.  It also allows the scanner light to dispurse and minimize scanner shadowing.

 
 
Keeping from squashing
The scanner lid can be a big problem. Usually we just tip down the lid and scan, but a size 12 Royal Wulff will not look good after a squash in the scanner. You can place a suitable object to hold the lid, but a better solution is a small stack of thick, white frames made from construction foam. Make a set of small frames out of white construction foam. The total thickness is 3/8" or 2 centimeters. Place the fly inside the white frame and lay 2 pieces of bright white laser paper on top as a reflective device.
The whole setup will not only keep the flies from being smashed, but also act as a reflector, dispersing the light, resulting in a better picture.

Other backgrounds
If you want a different color background, you can substitute the white paper for colored ditto - light blue or cream is preferable - but it is absolutely worth experimenting with other backgrounds such as textured paper, book covers, fabrics, plastics and materials like wood, bark or metal.
An alternative is to just leave the lid open! Depending on the room above the scanner, this will give you a pitch-black background or something quite dark. This is especially useful for light, translucent flies, which has a tendency to disappear on a white background. You can also experiment with backlight where a normal lamp casts a light on the fly on the glass plate of the open scanner. You will have to experiment with softening the light and moving the lamp out of the view of the scanner.
Mounting the flies in small objects such as cork, straw or small wooden sticks can give you control of their position and add to the dynamics in the picture.

Upside down
Many scanners will cast a shadow when scanning three-dimensional objects. This shadow will usually be on one side of the fly. Make sure that it is on the underside - making the light appear to come from above the fly. If it winds up on top of the fly, your fly will appear illuminated from below, which is very uncommon and strangely looking.
To correct the problem, you just rotate the fly 180 degrees horizontally in the scanner - turn it upside down.

Clean your scanner!
Many scanner glasses and lids are dusty and dirty. Use your normal household glass cleaning agent and a soft cloth or tissue and wipe off the glass and the inside of the lid. Make a prescan while the lid is open. This will reveal smudges or fingerprints, which otherwise can be hard to see.

 

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