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:

  • ImageJ/Fiji
  • NIS-Elements AR (from Nikon)
  • Volocity (from PerkinElmer)
  • Huygens (from SVI)

Huygens is a program mainly used for deconvolution. Deconvolution is a computational method by which the signal to noise ratio of images is increased (which means that even images suffering from noise will appear in good quality afterwards). Also, the (mainly axial) resolution is improved and the background reduced. Prerequisite to deconvolution is that images are "Nyquist sampled" in 3D (x, y and z): For a 100x NA 1.4 objective this means that the pixel size is between 50 and 80nm and the distance between the slices is about 150nm.
Huygens usage is free for all microscope users in the NIC. Users get a short introduction to the program on request (free of charge). Others may get access to Huygens for an annual fee of 80€. The program can be controlled by a web interface (the Huygens Remote Manager) and is hosted on our own server.

In order to open Images that were taken with NIS-Elements or Volocity in ImageJ a plugin called "Bio-Formats" is required. The latest release should be downloaded from this address: http://www.openmicroscopy.org/site/products/bio-formats/downloads. Just add the Bio-Formats library "bio-formats.jar" to ImageJ's plugins folder. Fiji contains this plugin by default.

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: 2017-04-12

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