Basic Concepts

The software completes all microscopes, microscope systems like LSM, and cameras from ZEISS to efficient and tailor-made imaging systems. With little training you will interactively control the entire workflow from image acquisition, processing and analysis.

Depending on the system you can capture single images, multi-channel fluorescence images or video sequences with up to 16-bit per channel image information. The software contains the so called "Smart Setup" which automatically delivers several proposals for the optimal dye and wavelength combinations for an experiment.

A wide range of different cameras can be used, starting from simple consumer cameras through to high-resolution and high-sensitivity microscope cameras. The seamless integration of cameras into the software allows you to acquire complex images and image sequences by one mouse click. For best results we recommend to use ZEISS Axiocam microscope cameras.

After acquiring an image, it is immediately displayed on your screen. It can then be optimized using a wide range of techniques:

• Contrast, brightness and color adjustment
• Noise suppression, smoothing and contour enhancement
• Sharpness enhancement/emphasizing of details
• Correction of illumination influences and white balance

The software can also be used to add any annotations that you may require to the images. All elements, from scale bars and colored markings through to text and graphics, have been integrated into the program.

Even with ZEN lite, you are able to perform simple interactive measurements. The measured values (e.g. lengths, areas, and perimeters) are made available in a data table and can be processed further using spreadsheet programs.

With the optional modules Image Analysis and Measurement, you can perform professional analysis tasks like generating automatic measurement procedures or measuring microscopic structures interactively.

For the ZEN software we developed a special file format called *.czi (Carl Zeiss Image). Besides the image data itself, the image format saves a lot of additional data, for example the date of acquisition, microscope settings, exposure values, size and scale details, contrast procedures which were used. Also, all annotations and measured values are saved with the file.

To learn more about the ZEISS image file format we recommend to visit the ZEISS Microscopy Community forum in the internet (http://forums.zeiss.com/microscopy/community/forum.php). There you can join interesting discussions or download the detailed documentation of the file format.

The extensions concept allows you to extend ZEN dynamically in its functionality. From a technical point of view the concept is comparable with plug-in`s or add-on`s. For the extensions we reserved a special area (Extensions tab) within the software so that you can find all loaded extensions at a glance.