Scanning films of different sizes: 110 and 126 films
The Super Coolscan 5000 is designed to scan 35mm film. If you buy an adaptor, it will also scan APS film.
Interestingly, Nikon make no real attempt to let you scan 110 or 126 film. This is despite the fact that both formats were available for decades and probably comprise a bigger share of the 'legacy' negatives that people would like to scan.
110 film can be scanned reasonably easily. 126 presents a problem.
126 is historically the older of the two formats, so I'll discuss it before going on the the (possibly) easier case of 110 film.
126 film
126 film was developed by Kodak and was popular in the 1960s and 1970s. Its film is exactly the same width as 35mm film: if you include the sprockets. It comes in a handy drop in cartridge which made cameras easy to load and meant that winding the film on was less difficult. Instead of having two large tractors of holes at the top and the bottom of the film, it only had much smaller sprocket holes on the bottom. This had two benefits: less film as wasted, and more film could be used to capture images.
(Film makers used to collect up the chads chopped out of film when the sprocket holes were added and recycle them. Waste not, want not.)
The statement 'more film could be used to capture images' causes the problem. 126 film renders its image right up close to the top of the film. The Coolscan can't go right up to that edge.
The 126 cameras created a square image, which isn't very normal for cameras. It's not often that you buy and display a square image. So if you decide to forgo the top 7-10% of your image, then you don't have much of a problem. But if your photographer had tightly framed the picture so that something important was at the top of the photo, then you are in BIG trouble. The head is chopped off.
If you turn the negative upside down, the head is STILL chopped off.
There's only one way to get the tops of heads back: and you have to swallow deeply before you do it.
You'll need to use your Nikon Strip Film holder FH-3.

'What?' (I hear you say) 'I don't have a Nikon Strip Film Holder FH-3. There wasn't one in the box with my Coolcan 5000.' Sad, but true.
The flat film holder shipped with the earlier scanners (like my original Coolscan LS-2000), but doesn't ship with the newer scanners. The film holder is meant to allow you to scan films that get stuck in the automatic film feeder mechanism. The film holder is dead cheap (in scanner terms) at less than US$20-40 from large US retailers. But Nikon preserved a little profit for itself by dropping it. Now you have to go and buy one: if you can find one. For example, the enormous photo super store (which stocks practically everything) B&H Photo Video doesn't seem to have one in stock today.
Your 126 film will be in strips of negatives: probably four pictures in a strip.
If you cut it into single negatives, you can then place the single negative into your Nikon Strip Film Holder FH-3. Sideways. You'll lose 5-8% of the left and right of your photo: but gain the top and bottom. (The amount you lose is probably about 1 or possibly 2mm on each side out of a negative 26mm by 26mm.) I guess if you really wanted the entire image, you could scan it both ways and stick it together again in a paint program. It would want ot be a good image to deserve that amount of effort, but it is theoretically possible.
By the way: after you have chopped your negatives into single images, you'll incur the wrath of photo imaging shops down the years who put those stern instructions on negative sleeves to NOT chop the negatives into single frames. On the other hand, I'm not sure whether a photo store would be able to do a print from a 126 film these days.
(It will also be tricky for you to store all those single negatives in negative sleeves.)
*Update 28th May 2007: Rescuing chopped heads**If you are extremely careful. you can position a strip of 126 negatives slightly off centre in a way that will allow you to scan almost to the top of the negatives. There's a groove in the black plastic recess that centres the negatives. Lift the negative over the edge of the negative until it touches the first protruding parts of the silver negative holder. Don't cross the silver bits. Your negative will normally not be damaged by sitting over the edge of the black grooves. Then, be careful when you insert your film into the scanner to make sure it stays in position.
110 film
By comparison with 126 film, 110 film is a walk in the park. Provided you have your Nikon Strip Film holder FH-3. (Discussed above.)
Carefully lay your negative down the centre of the holder and then crop the image. You'll be rewarded with a tremendously grainy underwhelming scan. It's not your scanner or your technique that is at fault. The 110 format was always dismal.
There are two things to be careful of:
Autofocussing
AutoexposureIf the film isn't centred, the focussing might not work. I haven't had a problem with focussing yet, but logically it could cause a problem.
More significantly: If autoexposure meters the entire 35mm negative area is used, then the white space (where the negative isn't) will lead to the negative being way too dark. Fortunately, once the negative has scanned (and is viewable as an image (rather than a preview) in the Nikon program) you can adjust the histogram. Click on the scanned image, and then set your dark/white spots and adjust the curve on the histogram window. The image is manipulated and can then be saved (instead of manipulating the preview, which will be unbalanced by the white space).
When I look at my 110 scans, I can see that the small negative size is one reason for the lack of final quality. But the scans are still a couple of thousand pixels in each direction. That ought to be enough to get a halfway decent image on a screen or on a 10x15cm print. But the lenses (and exposure system) on cheap 110 cameras from the 1970s and early 1980s pretty well sabotaged any change of good images. Plastic soft drink bottles would probably have created a better lens than the ones placed in these cameras. From the day I first got a 110 camera (to replace a 126 camera that had been quite usable, but which died of old age) until the day I replaced it with my Pentax ME Super 35mm SLR, I never liked my 110 camera.
The image below is sample of a bit of 110 film, showing all of negative 15, a sprocket hole in the white space between the pictures and a little bit of negative 14 (on the right). This image is much larger than the real negative, which is only 17mm high making a 110 negative just over one quarter the size of a 35mm negative.

* Update 28th May 2007: Treating your 110 negatives as slides **If you can't get your hands on the FH-3 film holder, there's another option. Cut your 110 negatives into single negatives, and put them in a slide holder for 35mm slides. Since the size of the slide holder is exactly the same as for a 35mm slide, it will slide into the Nikon slide feeder nicely. One company that still makes these holders is Gepe. See Gepe 110 Slide Mounts at B&H Photo Video.
Coolscan 9000 and other options
If your pockets are very deep, another possibility would be to buy the significantly more expensive Nikon Coolscan 9000ED. The 126 negatives might fit into the film holder for larger 120 sized film negatives.
110 negatives *might* fit into the optional holder for 16mm film available for the Coolscan 9000... except that 110 film is 17mm wide... so you would probably still be better off to use a larger negative holder.
Finally, the simplest approach might be to use a flat bed scanner. The quality is nowhere near as good as the Coolscans... but if the camera was cheap then the source negatives might not ever produce much better than a rough image.
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