Perl is cross-platform.

The first thing you have to wrroy about is the algorithm, and the language is not really that important. I can imagine what the algorithm does is just whole lots of math, Perl can do it, other languages can do it as well. Pick one that you are familiar with.

Study a little bit about image analysis, especuilly, texture analysis. Don't think internet helps much, too specific. You need some book in this area.

If you find some perlish solution to this task, I hope you'll be able to find a better way to do it.

For the roll-your-own option, perhaps you could look into more conventional image duplicate-finding approaches, some of which have been discussed here, e.g. by BrowserUk, though you'd need access to the raw scanner images, and have to experiment with the comparison to see if it can be tuned to be sensitive enough to find a reasonably small number of matches without deciding that all fingerprints in your database are matches. I'd think you'd use the fingerprint only as a first identifier, then prompt for a password, so the fingerprint tool need only narrow down your ID to a small number of potential matches in your database, not a single person.

Finally, as interesting as I find the problem, I must say I have serious doubts about biometrics, both in ethical and practical senses. For starters, even in my personal circle of friends and relatives I can count half a dozen missing digits. Then there is the recent suggestion that fingerprints are not so easy to accurately compare as has been thought (and indeed haven't really been properly investigated), and the now famous gelatine hack. Perhaps something like a hardware key would be easier and safer to implement in your instance?

Any passive security system can by bypassed given enough time, effort, and money. The object is just to make the cost of bypassing security higher than the gain, and unless you're doing high-stakes research or DoD work, a simple fingerprint / password system should be sufficient. Possible improvements might include:

Finger temperature scan and/or blood gas reading (former might be faked by warming gelatin, latter is much harder to)

Automatic digital photograph of the finger as it comes close to the scanner (if it looks odd, it's gelatin or has been cut off)

Weight plate (place feet here, test for weigh within x pounds of last scan with same fingerprint and pass)

Retinal scan (though if you have one, why do fingerprint?)

I certainly agree that anything can be broken, but I am particuarly wary of complex bleeding-edge (if you will) technology systems that appear to improve things (in this case security, but that isn't the only case), but really serve more to hide insecurities behind flash and sizzle.

Just to extend the argument a bit more:

• finger temperature scan - pointless as skin surface temperature is most certainly not constant enough in any individual to be useful as even a partial identifier
• blood gas reading - perhaps harder to fake, but why bother when like temperature, it too is not going to be consistent enough in a single user (did you have a beer at lunch?)
• automatic digital photograph of the finger as it comes close to the scanner - now there's some cool AI: first step, see if you can tell a moving finger from a moving sausage reliably in real time. Better attack: mount the gelatin on a real finger.
• weight plate - pretty crude, depends on clothing (seasonal), number of devices clipped to the subject geek, and whether they went to the all-you-can-eat down the street for lunch. Anyway, if you want to steal someone's finger, it's an easy matter to weigh them too.
• retinal scan - perhaps the best of the lot, but given the poor science behind finger prints, I'm similarly loath to assume these are correct. It also wouldn't surprise me if there are legal problems regarding employees with disabilities as there are with most biometrics.

I'm no expert and I've doubtless missed things, but my point is an RFID ID badge or similar with a suitably long encryption key and photo is far simpler, useable by both machine and human security staff, easy to issue, easy to confirm, and easy to cancel. I'm sure it too has truckloads of problems, but when we step past the intriguing academic exercise into practical application, simple wins with me every time.

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I'd like to be able to assign to an luser

There is no mention of Linux support on their website, but one review said there was Linux support for the reader. You could contact Identix directly to verify this.