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Why Micro-Manager

Nenad Amodaj, August 10, 2006

Software control of microscopes and associated hardware (shutters, filter wheels, stages, cameras, etc) has become very important in biological research. Currently, there is a large number of commercial software packages available, some produced by microscope or camera manufacturers, others by third parties. In fact, almost every hardware vendor pushes its own software package for microscopy. The industry seems to have reached the conclusion that you need to have your own in order to boost sales of your hardware and to simplify support. Viewing software as a vehicle for selling hardware or manipulating the competitors, led us to the situation where every company is almost forced to develop its own variation of the same software, over and over again.

In the situation where you already have too many choices, the decision to make yet another one, may seem contradictory. But, what we really have right now is that various hardware and software vendors are competing to supply the complete solution by attempting to provide all required software in a single package. Unfortunately, in automated imaging there is no such thing as the “complete solution,” and users are faced with a number of mutually incompatible software packages, each inadequate in its own way. Sometimes, due to some obscure technical incompatibilities you need to use two different software packages within the same hardware setup. You probably know the story: “To use camera X, I need software A, but device Y works only with software B”. Another problem with commercial packages is that they can not be easily extended to support new devices and novel acquisition techniques. You are pretty much dependent on the vendor for fixing problems, adding new functionality and supporting new (or legacy) devices.

In such circumstances there is an obvious need for more flexible and affordable solution. Open Source licensing of the software will enable unrestricted modifications and extensions of the functionality and device support, by various parties, both commercial and non-commercial. It creates the possibility for various users contributing their drivers and functionality extensions to the community. It also gives the device manufacturers the chance to supply (contribute or even sell) the best possible Micro-Manager drivers for their hardware, because they have full access to the source code. And finally system integrators may find it easier to provide customized turn-key solutions with Micro-Manager.