All of our Carl Zeiss confocal microscopes and the fluorescence correlation spectrometer use the Carl Zeiss AIM software. The software controls the hardware and has powerful image processing capabilities, including 3D visualization. The functionality can be extended using macros.
All images are saved as *.lsm files. Typically they are accessed through a *.mdb Microsoft Access database. The imaging parameters are stored within the image file as well as in the database. Images not associated with a database can be opened using the "File → Import" command. The images can be exported in a variety of file formats, including *.tiff, *.jpg and *.avi. Because exported images loose all the imaging specific information, one should always keep original files.
The software can be used in online mode at the microscopes and offline at any Windows 2000 computer. To run the software a licence is required. A free version called "Image Browser" with reduced functionality is available.
The Carl Zeiss AxioVision software uses the different *.zvi file format. Confocal images can be imported or exported into AxioVision and vice versa. The free AxioVision software package is called "AxioVision LE".
The functionality of the AIM software can be extended using macros. They can be accessed using the "Macro" menu. The assignment is user specific, thus macros might be installed at the system but not be visible for the individual users. Use the "Macro → Macro..." command to add specific macros to your login. Usually macros can be found in the folder C:AIM/Macros. Make sure to use macros with the same version number as the AIM software you are using. Additional macros can be downloaded from the Carl Zeiss Web page or the Carl Zeiss ftp server. For ftp access the username is the serial number of a Carl Zeiss confocal microscope and the password is the number of the associated dongle.
The easiest way to write macros is to use the "Visual Macro Editor" at "Macro → Visual Macro". A macro is assembled by dragging building blocks into "Program flow" or "Data flow" cells. The blocks are connected by red program flow or blue data flow connections. After the selection of a block, function specific parameters are accessible. Often they can be read back (copied) from associated control windows. Most of the parameters can be associated with variables and mathematical expressions.
More sophisticated macros are written in Visual Basics for Applications (VBA).
Our fluorescence correlation spectrometer Carl Zeiss ConfoCor 3 uses software based on the AIM confocal microscopy software with FCS specific additions. It controls the hardware and allows fitting of correlation functions.
FCS Viewer for Raw-Data Files
The software can save raw data files describing the arrival time of each detected photon. The file format was changed when upgrading from software version 3.2 to 4.0. We have written a program to inspect the raw data software version 3.2.
Bug Fix for FCS Data Copy
Within the Carl Zeiss ConfoCor 3 software, measurement results can be copied between different windows. After saving and opening the data file, a bug in the software prevents the display of the data. This small piece of software fixes the saved data file.
ImageJ is the Java version of the popular free NIH Image software. It is platform independent. The source code is available. Its functionality can be extended using easy to write macros and plugins. There is a huge user community and for almost all microscope image processing needs solutions are available.
IDL is a programming language optimized for image processing. Typically programs run in a programming environment, but it is possible to write stand-alone applications.
Users of IDL at the Stowers Institute can discuss programming questions with IDL specialists using the Stowers Portal at ITT (the producer of IDL). To get access please contact Earl Glynn.
At the Stowers Institute we have several licenses.
