system design & development

TEMRAI beholds the whole system for remote operation of a Transmission Electron Microscope. Such as video streaming, remote control protocol, interaction protocol and user friendly interface.

TEM Interaction Protocol

The interaction between the user and Transmission electron microscope was analysed in a qualitative observational study. The user was observed while working with the microscope and all the actions were recorded and logged.

Out of this study commonalities between the actions taken by all the users could be found. These commonalities can be summed up in a simple protocol which can be a good base for development of future user interfaces and software for TEM users.

This protocol consists out of four steps, microscope preparation, specimen searching, image acquisition and gathering analytical data ( see figure below ).



During prepararation time can be gained by intelligent microscope set up. Instead of a tab structure in the current microscope interface the user is presented with a microscope overview by pressing a specific element of the microscope the user gets to see only the relevant settings.
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Remote desktop

Not all microscope settings and variables can be accessed from a remote location, to facilitate the advanced TEM users a remote desktop viewer is build into the flash user interface. Access to the remote desktop is restricted to advanced users.
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During the search step the user is provide with different ways to navigate the specimen. One of these tools is the grid overview the grid overview shows the user the current position of the specimen and the size of the viewing area. The magnification can be change by scaling the viewing area handlers and the position can be changed by dragging the handler.
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Positions can be stored during the search step and each position holds all the relevant microscope parameters to be able to retrieve the same image as at the time of storing the position. Positions are shown as small thumbnails on a special positions page and in are shown in the grid overview.
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Other ways to manipulate the specimen and handle specimen navigation is through tools shown over the live streamed image of the specimen. This will give the user the feeling of directly manipulating the specimen.
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When having found all the area's of interest the user will be able to acquire image through the microscopes different CCD camera's and detectors. Images can also be acquired in series. In the future more intelligent ways of image acquisition should be build in, such as automatic acquisition of all or selected images.
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TEM Remoting Server

To be able to control the microscope from a remote location an communications interface should be available to a remote application. The first attempt using a dot net webservice was very promissing, but after further testing and better transparancy of the service the decision was made to write a server from the ground up using a defined protocol, which can be used as a standard for future tem remoting servers.

The server was developed using tcl/tk and implements the TEM remoting protocol. The server was tested an retrieving all microscope parameters took no more than 160 ms, this was about the equivilant of one call using dot net webservices.

Real-time image streaming

One of the major bottle neck in remote microscopy is or actually was Real-time image streaming. Image from the specimen should be streamed over the internet with as low a latency as possible. In my trail and error sessions I found that the streaming the image through the flash com server worked best and had a latency that was low enough for searching the specimen. The latency of the image of the specimen was 180 ms at 90% image quality with 15 frames per second for a resolution of 640 x 480 pixels. This means that the biggest bottleneck in remote microscopy is no more. In the latest release the RED5 open source streaming server was used.