Imaging Analysis and Visualization Software

Available on computer in 209

Amira (Visualization Science Group)
Amira offers 3D image analysis and visualization for a wide variety of image data, including confocal light microscopy, CT and MicroCT, MRI, lightsheet, OPT, etc. It provides tools for image segmentation, 2D and 3D volumetric measurements, 3D reconstruction from 2D section data and neuron tracing.

Imaris (BitPlane)
Imaris enables 2D–4D image analysis and visualization. Analysis includes cell counting, cell tracking, neuron tracing image segmentation, co-localization and 4D movie generation.

VGStudio (VolumeGraphics)
VG Studio is sophisticated volume rendering software that enables fine control of visualizations through the manipulation of transfer functions, lights and shadows and a variety of rendering procedures.

Huygens Essential (Scientific Volume Imaging (SVI))
Huygens image processing and image analysis software for deconvolution, colocalization, object analysis and visualization. Huygens supports file formats from most major microscope manufactures.

SyGlass is an immersive visualization and annotation system for volumetric data. SyGlass can visualize 3D surface data and multi-channel volumetric data from wide variety of imaging modalities including CT, MRI, 3&4 D optical microscopy (including Lightsheet, OPT, confocal & multiphoton microscopy) and serial EM.

Free downloads

FIJI (FIJI Is Just ImageJ) is the “go to” imaging application for general purpose image processing. FIJI uses the BioFormats library and can open most vendor specific image file formats. Many image analysis tools and scripts have been written for FIJI. Though the user interface is less refined than commercial software, FIJI performs equally well in many cases. FIJI can be found at:

LAS-X (Leica Microsystems)
LAS-X is software for viewing native Leica image files. LAS-X can be used to convert Leica’s .lif files to standard image formats as well as provide some image processing and analysis tools. LAS-X can be found at:

ZEN Lite (Zeiss Micrscopy)
Zen Lite facilitates the viewing of Zeiss native file formats, including .zvi, .czi and .lsm, and the conversion of images to standard formats from Zeiss formats. Download Zen from: