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Acquisition
Our lab relies extensively uses advanced light microscopes. To execute experiments
with such equipment, one needs software control of the camera and all motorized
components (such as shutters, filter wheels. Z-drives, etc..). Our lab has used
a great number of commercial software packages for this purpose in the past.
We were forced to use this many different packages since not a single one was
capable of supporting all the imaging hardware used in the lab. Having to work
with a multitude of different user interfaces, and having to discover the quirks
of many different software packages is not a pleasant experience for the post-docs
and grad students in the lab. Most of these software packages only run under
Windows (and lots of us like Macs). Moreover, we have run into many instances
where the software used was simply not capable of executing the experiment we
had in mind.
To remedy this situation we started a project to create an Open Source, cross-platform
software for image acquisition. We were extremely lucky to interest Nenad Amodaj,
who is a gifted and experienced software engineer, in the project. Nick Endres
came up with name "Micro-Manager." The software was developed in close
collaboration with post-docs and grad students in the lab. As a result, the
software is really easy to use for Cell Biologists. The
Micro-Manager project released version 1 of the code in January 2007. We
are running all our wide-field systems now with Micro-Manager.
Analysis
Rather than relying on "pre-cooked", "black box" solutions,
the lab uses or writes openly accessible solutions. There are three major platforms
that we use:
- Nico Stuurman, March 2007
updated 4/9/07
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