Software

Microscope Setup Tutorials

Use this link to familarize yourself with any microsocpe at HCBI and setting up its acquisition parameters.

ZEN

For a free copy of ZEN lite image processing software, click here: ZEN lite (Windows only).  The HCBI recommends frequent downloads of ZEN to ensure your software is up-to-date and compatible with files from our newest microscopes

Click here to download the ZEN Blue Image analysis guide.

Fiji/ImageJ

For a free copy of Fiji (ImageJ) image processing software, click here: Fiji (Windows or Mac)

Click here to be redirected to the extensive Fiji online documentation
Click here for a link to the ImageJ 1 documentation

Lightsheet .CZI to .TIF converter

The .czi to .tif converter for Lightsheet files is implemented as a Fiji/ImageJ macro. Click here for download, installation and help documents for timelapse/multiview files, and here for tiled files.

AxioScan .CZI to .TIF converter

The .czi to .tif converter for Axioscan files is implemented as a Fiji/ImageJ macro. Click here to download the macro script. Make sure your Bioformats plugin is installed and up to date (5.7.2 recomended).

Volocity

Click here to view the Volocity User Guide

IMARIS

Click here to download the IMARIS Reference Guide.
Click here to visit the IMARIS Learning Center