Integrated Light Microscopy Core

Image Processing

Display and generate data from images
ImageJ/Fiji Classes

Image Processing Software

The Core Facility is available to help users display and analyze their light microscopy datasets.  We use and teach both pay-to-play and open source software packages for reconstructing, displaying, deconvolving, and quantifying image data.  Our resources for open source software, particularly ImageJ, are freely available to everyone.  Our paid image processing software packages are on high-end workstations in the facility and are available for a small hourly workstation use fee.


3D and 4D Rendering and Analysis

Imaris is powerful multi-dimensional image processing software. Ideal for multi-dimensional rendering, neurite tracing, spine counts, and multi-dimensional measurements (volume, area, 3D counts, etc).

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Huygens Deconvolution Software

Huygens Pro from SVI (64-bit Windows Server, available by remote desktop) — Our prefered deconvolution package. Our pacakge includes the module for STED deconvolution!

Huygens Pro is available on the Windows 64-bit server workstation in KCBD 1250 or by remote desktop from any UChicago network computer.

Arivis Vision 4D

Rendering and Analysis of Big Data

Arivis Vision 4D from arivisAR is modular software for working with multi-channel 2D, 3D and 4D datasets of almost unlimited size, independent of available RAM.  Particularly suited to large (>1TB) data from high speed confocal, lightsheet and 2-photon systems.

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Other Pay and Open Source Software Packages

The Core maintains workstations running offline versions of our image collection software, including Leica’s LAS_AF and LAS_X, Zeiss Zen and 3i Slidebook. We also provide a MatLab license and support and training to users analyzing data in open source software, particularly ImageJ / Fiji and QuPath packages.

These packages are available on several Core workstations, and the open source software can be downloaded onto any computer.