Image processing, visualization and analysis

Software packages available in LMCF

duke lmcf imaris Imaris with several analysis modules: Imaris, MeasurementPro, Imaris Track, Imaris Colocalization, In Press, Filament Tracer, Vantage and Imaris XT (Matlab) are available on both FFSC64bit and Nan Duke workstations.
duke lmcf metamorph

MetaMorph Premier (4 offline licenses FFSC 64bit, LSRC workstation 2, Nan Duke workstation and RP2 workstation) - Tracking, 4Dviewer, count nuclei, neurite outgrowth etc applications. MetaMorph Basic (1 license - LSRC WS1 64bit) - core functions with MDA review but no App modules.

duke lmcf huygens Huygens Essential deconvolution from SVI with options for widefield, confocal, multiphoton, spinning disk and timeseries all running with 8 threads. PSF distiller allows the use of measured PSFs. Batch deconvolution. 3D visualization, colocalization and analysis. LSRC 64bit workstation 1.
duke lmcf volocity Volocity - Visualization and quantitation/measurements for 3D and 4D data. Colocalization and tracking. Two copies - LSRC 64-bit WS1 and Nan Duke workstation.

And ImageJ/FIJI, Zeiss (Zen) 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 1 (C136-B 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 5 - visualization and quantitation/measurements/tracking modules
  • FIJI ImageJ 64-bit
  • Office 2013

FFSC-64 bit workstation (4226 FFSC)

  • Imaris 7.7
  • MetaMorph Premier (system ID 32331) - Tracking, Count nuclei, neurite outgrowth etc applications
  • MATLAB
  • FIJI ImageJ 64bit
  • Zen lite
  • Office 2013

LSRC workstation 2 (C136-B LSRC)

  • MetaMorph Premier (system ID 32672) - Tracking, Count nuclei, neurite outgrowth etc applications
  • LAS AF (Leica SP5 confocal and TIRF)
  • Zeiss Zen lite
  • Adobe Creative Cloud - Photoshop, Illustrator, Lightroom, Premiere Pro
  • FIJI ImageJ
  • Office 2010

Nanaline Duke workstation (337A Nan Duke)

  • Imaris 7.6
  • Volocity 6 (4100114)
  • MetaMorph Premier (system ID 10199) - Tracking, Count nuclei, neurite outgrowth etc applications
  • FIJI ImageJ 64bit
  • Zeiss Zen 2010 offline
  • Leica LAS AF SP8 offline
  • Office 2010

DeltaVision Offline deconvolution (4226 FFSC)

  • DeltaVision SoftWorx deconvolution software
  • FIJI ImageJ 64bit
  • OpenOffice

RP2 workstation (111 RP2)

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

Software for your own computer

imageJ
FIJI (FIJI Is Just ImageJ)
FIJI is a version of ImageJ with prepacked plugins and a few other tweaks FIJI - Fiji is just imageJ

imageJ
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, Linux and PC. ImageJ site
zeiss image browser
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 710/780 confocals (also opens .lsm files from the 510 AIM software). PC only. Download
leica las af lite
Leica LAS AF lite
Free version of the Leica confocal LAS AF software for your own computer. PC only. Download from Leica.
irfanview
Irfanview
Free program
that can open a large variety of image file formats. PC only.