Commercial and academic image analysis software​

https://imaris.oxinst.com/products/imaris-for-core-facilities

Imaris Software by Bitplane is an interactive visualization and analysis software for 3D and time-lapse microscopic images. It offers a wizard-driven interface providing a clean and straight forward way of segmenting and quantifying objects of interest in 3D and with time. It is suitable for processing big datasets and provides a plethora of quantifications characterizing cell and object shapes, intensities and colocalizations.

The Core Facility Package is built around the main Imaris Core supporting 3D/4D rendering, object detection and snapshots/animations, and includes the following:

• Four segmentation modules: ‘Spots’ to segment spot-like structures, ‘Surfaces’ to segment any shape of structures, ‘Cell’ to segment and analyze cells and their compartments, and ‘Filament Tracer’ to trace filamentous structures like neurons and vessels,
• Measurements Pro -to report and interact with detected object measurements
• Coloc – to visualize and quantify colocalized regions
• Vantage – to plot in 1D-4D and compare groups with statistical tests
• Tracking  - to track motion in 2D/3D, detect divisions and create lineage tree
• ClearView GPU-accelerated Deconvolution, 
• Stitcher - to precisely align and stitch multiple image tiles
• Batch – to process multiple images based on saved protocols for batch analysis
• XT to customize analysis with Matlab, Python, Java

Download

Free Imaris Viewer (for displaying raw images, Imaris segmentation images, making snapshots and simple animations)

Image Converter (to pre-covert raw images to Imaris IMS format) 

Explore Imaris learning resources.

https://www.moleculardevices.com/products/cellular-imaging-systems/acquisition-and-analysis-software/metamorph-microscopy

 MetaMorph is a very well-established software in microscopy offering quantitative image analysis tools from simple intensity logging to advanced morphometry analysis and assay-specific measurements. Software supports a variety of image display and processing tools suitable for 2D, 3D and time-lapse acquisitions. It also offers optional Application Modules, such as Angiogenesis Tube Formation, Cell Scoring, Cell Cycle Nuclei Count, Mitotic index, Multi wavelength Cell Scoring, and  Neurite Outgrowth analysis. It supports semi-automated analysis via journaling. 

Download MetaMorph help guides:

• MetaMorph 7.6 Visual Basic Reference Guide
• MetaMorph Basic Commands
• MetaMorph Dropin Commands
• MetaMorph 3D Module Commands

https://indicalab.com/halo/

Halo Imaging Software by IndicaLabs  is an image analysis platform for 2D quantitative image analysis. It supports fluorescence and brightfield images and reports morphological and multiplexed expression data on a cell-by-cell basis across entire tissue sections. Halo supports automate tissue segmentation, advance spatial analysis with custom filtering and classification, deconvolution, and unlimited channel display supported by the HighPlex FL module.

https://www.sci.utah.edu/software/fluorender.html

FluoRender is an interactive rendering tool for multi-channel fluorescence microscopy data visualization and analysis. It combines the rendering of multi-channel volume data and polygon mesh data, where the properties of each dataset can be adjusted independently and quickly. Fluorender futures clustering and tracking algorithms. The tool is designed especially for neurobiologists, allowing them to better visualize confocal data from fluorescently-stained brains, but it is also useful for other biological samples. 

FluoRender is available for free and is open source under the MIT License.

Download FluoRender 

https://www.microscope.healthcare.nikon.com/products/software/nis-elements

NIS Elements by Nikon is a complete software platform for Nikon microscopes control. It combines image acquisition, display,  processing, analysis, and data sharing. A full version of the software is available on the Nikon live cell imaging system and on a dedicated workstation.

For displaying, reviewing and exporting ND images from your office or home computer, download a free NIS Elements Image Viewer.

https://www.leica-microsystems.com/products/microscope-software/p/leica-las-x-ls/

Leica Application Suite X (LAS X) is the one software platform for all Leica microscopes. Software combines data acquisition with image processing and data analysis. A full version of the software supporting image analysis is available on both Leica microscopes and a dedicated workstation. For reviewing, displaying your data and simple image processing, download a free LASX Image Viewer. You will need to run it in a simulator mode.

https://voxx.sitehost.iu.edu/

Voxx is a voxel-based volume rendering software for 3D microscopy developed by Jeff Clendenon and Jason Byars at ICBM. This software permits researchers to perform near real-time rendering of large microscopy data sets on inexpensive personal computers. It was developed to explore 3D datasets collected on confocal and multiphoton microscopy systems, but it can also render other kinds of data (e.g. CT, MRI, etc.).

Voxx program exe file (but not the source code) is freely available for non-commercial use. However, Voxx is not open source. It is owned by Indiana University, and anyone interested in commercial applications and/or source code licenses should contact us.

There is no manual for Voxx2, but there is a Help command in the program. You can also review Jeff Clendenon’s 2015 presentation on 3D visualization and Analysis. 

Download Voxx

https://iss.com/microscopy/software/vistavision.html

VistaVision is a complete software package for instrument control, data acquisition and data processing for ISS FLIM systems. A full version of the software is available on the FLIM-PIE and 2P-FLIM systems.

The BZ-X800 Analyzer is an image measurement and analysis software package for the BX-800 All-in-One Fluorescence Microscope. It offers a wide range of image processing functions including stitching of tile-images, automated counting and quantifying target area within an image, and processing time-lapse data from single or multiple fields scattered across a wide area.

Keyence analyzer is available on the Keyence acquisition computer only.

IMART—Intravital Motion Artifact Reduction Tool—is a software tool for removing motion artifacts from intravital microscopy images collected in time series or in three dimensions. Developed by Kevin Lorenz and Edward Delp (Purdue University) and Paul Salama (IUPUI), IMART software is available for free download, and can be obtained by sending a email request to imart@ecn.purdue.edu.

https://imagej.net/plugins/vtea

VTEA—Volumetric Tissue Exploration and Analysis—is an ImageJ/Fiji plugin for three-dimensional tissue cytometry (3DTC), which enables the quantitative measurement of whole cells while retaining their morphology, localization and associations.

Download the VTEA plugin

https://www.olympus-lifescience.com/zh/downloads/detail-iframe/?0%5Bdownloads%5D%5Bid%5D=847249651

This software reads data captured by the FV1000 confocal-multiphoton microscope. Images saved with FV file format (OIF, OIB, FV multi-TIFF) can be read and exported in the common file formats (BITMAP, JPEG, PNG, TIFF etc.). This software is for data reading only, the full version of the software supporting image capture, measurement, analysis, 3D function etc. can be accessed on the Olympus FV1000 acquisition computer.

Download the viewer installation file 

https://fiji.sc/

Fiji is an open-source image processing package based on ImageJ2. Fiji implement a large variety of standard processing tools and includes many pre-installed plugins and macros for custom and advanced analysis tools. As an open-source platform, end-users have access to the code for verification and customization of tools. Fiji includes the Bio-Formats plugin, which allows it to open the majority of the proprietary file formats that microscope vendors use to store images and has a built-in macro that keeps the software up-to-date.

Download Fiji