Image Analysis

The images our users take in the NIC may also be analyzed there. The center has a computer room (U03) with image analysis workstations. Data can be analyzed with:

  • NIS-Elements AR (from Nikon)
  • Volocity (from PerkinElmer)
  • Huygens (from SVI)
  • Arivis Vision 4D (Arivis AG)
  • ImageJ/Fiji

NIS-Elements in the "Advanced Research" (AR)-version from Nikon is the central program for image acquisition and analysis in the NIC. It handles multi-dimensional imaging flawlessly, with support for capture, display, peripheral device control, data management and analysis of up to six dimensions (X,Y,Z, Lambda (wavelength), T, multipoint). It also offers sophisticated image processing features, such as an extremely powerful deconvolution module, exclusive one-click database capability, and Extended Depth of Focus function. All users of the NIC may use NIS-Elements as analysis software on several workstations in the center.

Widefield image before deconvolution
Widefield image after deconvolution with NIS-Elements 5.02

Volocity from PerkinElmer is the acquisition software used for our spinning disk microscopes (ERS-6 + VoX-Ti). Apart from image acquisition we're offering the software in a analysis license. It may be used in the NIC or from outside after getting granted connection to our license server.

Huygens from Scientific Volume Imaging (SVI) is a powerful deconvolution software that is controlled by a web interface (the Huygens Remote Manager) which means that you may up- and download your data and control Huygens from outside the NIC. Since August 2017 it runs on a server with 2 10-core Xeon CPUs and 1 TByte of RAM. It can be used in a batch mode, deconvolving many big data files sequentially without user interaction.
Huygens usage is free for all microscope users in the NIC after a short introduction to the program on request (free of charge). Others may get access to Huygens for an annual fee of 80€ (please contact me).

Spindle before and after deconvolution
Spindle before and after deconvolution

Arivis Vision4D is a modular software for working with multi-channel 2D, 3D and 4D images of almost unlimited size independent of available RAM. In the NIC we mainly use it to process images acquired by our new SPIM microscope, the LaVision Ultramicroscope II. The program has tools for stitching and alignment to create large multi-dimensional image stacks and offers a powerful analysis pipeline for 3D /4D image analysis (segmentation, tracking, annotation, quantitative measurement and statistics, etc). It runs on a powerful workstation with a 10 core Intel i7 CPU with 128 GByte RAM and GPU acceleration with 4 NVIDIA GeForce Titan X (Pascal) 12 GByte graphic cards.

Users who prefer to analyze their data acquired in the NIC in their own lab may use the free software Fiji, that is able to open data from NIS-Elements or Volocity (this requires a plugin called "Bio-Formats" that is included with Fiji).
A tutorial describing Fiji, written by Peter Bankhead, former image analysis specialist of the NIC, can be downloaded here. In case of questions you may contact Pete by e-mail.

If you need assistance for bio-informatics or bio-image analysis you may contact the CellNetworks Math Clinic-Team.

 

Bearbeiter: Christian Ackermann

Latest Revision: 2017-11-21

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