Processing optical microscopy files

Images taken with optical microscopes including our widefield (Zeiss Axio Observer 7 Inverted Microscope) and confocal (Zeiss LSM 900, Leica SP5) should be saved as the native file type, which is “.czi” for Zeiss and “.lif” for Leica. The native file type contains important metadata including instrument settings and image scale.  To view and process these specialized formats on your personal computer, you can use several free software programs including Fiji (for both native file types), Zen Lite (for Zeiss images only) or Imaris Viewer (for both native file types). You can also use the Image Processing and Analysis workstation in the ILSB to process your files, which has the licensed, more powerful versions of Zen and Imaris software, as well as Fiji.

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.