Software

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

Axio Scan .CZI to .TIF converter

The .czi to .tif or .bigtif converter can now be downloaded here.  This converter only works for .czi files acquired on the Axio Scan using JPEGXR compression.  A PDF file with extensive documentation is included with the download.

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.

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

Fiji Plugins:

Below are links to ImageJ plugins not included in the Fiji distribution that we have highlighted in various HCBI presentations:

Diffraction PSF 3D Generates Theoretical Point Spread Functions for deconvolution
DeconvolutionLab Deconvolves images with a user supplied PSF (theoretical or measured)
3D Object Counter Counts objects in a 3D image

volocityuserguide.pdf7.78 MB
image_analysis_guide_revised_01-2014.pdf946 KB