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Fluorescence Image Processing

Fluorescence microscopy images taken with the Zeiss LSM 900 and the Leica SP5 confocals are typically saved as native file types. These file types, .czi (Zeiss) and .lif (Leica), contain metadata including instrument settings and image scale.  To view and process these images, you will need to use either Fiji (for all native file types) or Zen Lite (for Zeiss images only).

Note: Standard ImageJ will not open .czi files (or any other native life science files) without the Bio-Formats plugin. To ensure your image will open, use Fiji rather than standard ImageJ.

For information on how to download and use Fiji, please see our Fiji User Guide.

For more information on how to download a temporary license of Zen Lite, please request a free trial with Zeiss.