Duke University Light Microscopy Core Facility - Image analysis and processing

Image processing, visualization and analysis

Software packages available in LMCF

	Imaris with several analysis modules: Imaris, MeasurementPro, Imaris Track, Imaris Colocalization, In Press, Filament Tracer and Imaris XT are available on FFSC64bit. Imaris, MeasurementPro and In press are available on the Nan Duke workstation.
	MetaMorph Premier (4 offline licenses FFSC 64bit, LSRC 32bit, Nan Duke workstation and RP2 workstation) - Tracking, 4Dviewer, count nuclei, neurite outgrowth etc applications. MetaMorph Basic (1 license - LSRC64bit) - core functions with MDA review but no App modules.
	Volocity -Visualization and quantitation/measurements for 3D and 4D data. Colocalization and tracking. Two copies - LSRC 64-bit and Nan Duke workstation.
	Huygens Essential deconvolution from SVI with options for widefield, confocal, multiphoton, spinning disk and timeseries all running with 8 threads. Batch deconvolution. 3D visualization, colocalization and analysis.
Avizo - Versatile data visualization software. Duke has a site licence for Avizo and we have these available in LMCF as a convenience. And ImageJ/FIJI, Photoshop, Illustrator, Zeiss and Leica offline, Excel, MatLab and various other useful tools that are free or commonly available are provided for convenience.

Image analysis workstations: what software is on each computer

LSRC-64 bit workstation (C138 LSRC)

Huygens SVI deconvolution, 3D visualization/analysis
MetaMorph Basic (System ID 10415) - all the features of the other MM workstations except no App modules.
Volocity - visualization and quantitation/measurements/tracking modules
Amira and Avizo
FIJI ImageJ 64-bit
Office 2003

FFSC-64 bit workstation (4226 FFSC)

Imaris 7.3
MetaMorph Premier (system ID 32331) - Tracking, Count nuclei, neurite outgrowth etc applications
MATLAB
FIJI ImageJ 64bit
Zeiss and Leica offline software
Office 2003
Photoshop and Illustrator CS4

LSRC-32 bit workstation (C138 LSRC)

MetaMorph Premier (system ID 32672) - Tracking, Count nuclei, neurite outgrowth etc applications
LAS AF (Leica SP5 confocal and TIRF)
Zeiss LSM Image Browser (Zeiss 510 confocals)
Photoshop CS2
FIJI ImageJ
Office 2003

Nanaline Duke workstation (337A Nan Duke)

Imaris 7.3
Volocity 6.0 (4100114)
MetaMorph Premier (system ID 10199) - Tracking, Count nuclei, neurite outgrowth etc applications
FIJI ImageJ 64bit
Zeiss Zen 2009 offline
Office 2010

DeltaVision Offline deconvolution (4226 FFSC)

RP2 workstation (111 RP2)

MetaMorph Premier (system ID 35364) - Tracking, Count nuclei, neurite outgrowth etc applications
FIJI ImageJ 64bit
Zeiss offline software
Office 2007

Software for your own computer

	FIJI (FIJI Is Just ImageJ) FIJI is a version of ImageJ with prepacked plugins and a few other tweaks FIJI - Fiji is just imageJ MBF ImageJ for Microscopy is another useful version of ImageJ with preselected plugins
	Image J Free software for image analysis, a Java based version of NIH image, versatile and many plugins are available. Available for Mac OS X and 9, Linux and PC. ImageJ download \| ImageJ plugins\| ImageJ documentation
	Zeiss free offline software Zeiss AIM LSM Image Browser for viewing files acquired on the Zeiss 510 confocals. PC only. Download (5 MB) Zeiss Zen software for the 780 confocal (also opens .lsm files from the 510 AIM software). PC only. Download (86 MB)
	Leica LAS AF lite Free version of the Leica confocal LAS AF software for your own computer. PC only. Download (58 MB)
	Photoshop Probably already available in your lab, can do almost anything but make sure you know what you are doing to your data. Some tips are here. GIMP is an open-source, free equivalent of photoshop for Mac, PC and Linux.
	Irfanview Free program that can open a large variety of image file formats. PC only.
	Quicktime Versatile program that is useful for playing movies.

Information and help with . . .