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The Microscopy Toolbox for Matlab

What is it?
It's a matlab toolbox that provides a conceptually different way to operate microscopes.
The idea is to allow the computer to have full control of the image acquisition process. The type of control starts with a relativly simple acquisition of x random sites in a well but can also be extended to a more sophisticated processes that combine image analsys during the acquisition process.

What is it good for?
You will be able to use the toolbox to build roboscopes. For more detalis please read the propoganda.

What makes it different?
The toolbox combines different classes and functions that allow the user to control a microscope by writing short pieces of computer code. Altough other enviroments allow writing macros or short scripts to control acquisition (e.g. journal...), those tools are usualy limited and were not designed for extensive use.

How do you do it?
The toolbox relays heavily on the micro-manager project. To some degree it can be thought of as an extenstion of that project.  The micro-manager base allows us to control all the different microscope parts. The advantage is that the list of supported hardware is growing pretty fast.

How is the toolbox designed?
The toolbox is implemented using Matlab object oriented capabilities. The main object is a Scope object that control all the aspects of the actuall microscope. The user need to define Tasks (another Class) and add then to the Scope. The scope will then decide on the optimal order in which to perform those tasks and will do that as quickly as possible.
All the images that are acquired are saved as OME-Tiffs


Function documentation