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.
Imaris
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).
Imaris workstation
UChicago users- 64-bit Windows 10
- Intel Xenon CPU E5-2697 v3
- dual 2.6 GHz processors
- 512 GB of RAM
- 30TB dedicated storage
- Software includes Imaris 9.1.2, Imaris File Converter, Arivis Vision 4D, FIJI, ChimeraX, MatLab, Ms office, SlideBook 6.0 Reader, FluoRender and IrfanView
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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.
Huygens workstation
UChicago UsersArivis 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.
Arivis workstation
UChicago Users- Precision 7920 Windows 10 workstation with dual Intel Xeon Platinum 8168 processors (48 cores)
- 1 TB of DDR4 RAM
- Nvidia Quadro RTX6000, 24GB GDDR6 graphics (4608 CUDA, 576 tensor, 72 RT cores)
- 70TB dedicated storage
- Software includes Arivis Vision4D analysis suite, Matlab, FIJI, Qupath, MS office, and ChimeraX
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Other Software Packages
The Core has workstations running offline Leica LAS_AF and LAS_X, 3i Slidebook and Olympus OlyVIA. We also support users analyzing data in free, open source software, particularly ImageJ, Fiji and QuPath.
These packages are available on most Core workstations, and the open source software can be downloaded onto any computer.