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Software - Imaging


AutoQuant offers the most powerful deconvolution tools available for life science research. Retrieve better data from your images using the most complete suite of 2D and 3D algorithms available. It offers an advanced Blind Deconvolution algorithm which is both iterative and constrained.

Software Homepage:
Available on: Windows workstation CBIWS10
Note: AutoQuant is an older version with a bug that requires admin permission to run. Please see staff to use AutoQuant.


BioImageXD is a free open source software package for analyzing, processing and visualizing multi-dimensional microscopy images. It can be used for simple visualization of multi-channel temporal image stacks to complex 3D rendering of multiple channels at once. Image processing tools include deconvolution, registration and tens of tools for mathematical and logical processing and noise reduction.

Software Homepage:
Available on: Windows workstations CBIWS15 and Kocher


ImageJ is a public domain, Java-based image processing program developed at the National Institutes of Health. ImageJ can display, edit, analyze, process, save, and print 8-bit color and grayscale, 16-bit integer, and 32-bit floating point images. It can read many image formats including TIFF, PNG, GIF, JPEG, BMP, DICOM, FITS, as well as raw formats. ImageJ supports image stacks, a series of images that share a single window, and it is multithreaded, so time-consuming operations can be performed in parallel on multi-CPU hardware. ImageJ can calculate area and pixel value statistics of user-defined selections and intensity thresholded objects. It can measure distances and angles. It can create density histograms and line profile plots. It supports standard image processing functions such as logical and arithmetical operations between images, contrast manipulation, convolution, Fourier analysis, sharpening, smoothing, edge detection, and median filtering. It does geometric transformations such as scaling, rotation, and flips. The program supports any number of images simultaneously, limited only by available memory.

Software Homepage:
Available on: Windows workstations CBIWS15 and Kocher
Plugins: Besides the default available plugins, we have the following installed:
- DeconvolutionLab
- Parallel Spectral, Iterative, and HRRT Deconvolution from Piotr Wendykier
- Iterative and Iterative3D Deconvolve and Convolve3d from Bob Dougherty
- PSF Generator


Imaris allows visualization of original and derived data objects in a real time interactive manner so you can quickly make visual assessments of your experiments in 3D and 4D to discover relationships that are otherwise hidden.
Note: When first running Imaris, it will ask for how much memory is available on the graphics card. To find this value for the workstation, right click on the desktop and select Nvidia Control Panel. When it opens, go to Help>System Information and there it will display the graphics card memory.
Note: Current version is 7.6. Older versions are available for legacy purposes only, no support available.

Software Homepage:
Available on: Windows workstations CBIWS15 and Kocher