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Data Management 

Data Formatting

We highly recommend that all data is saved in Nikon's proprietary *.nd2 (or *.ics) format. This format stores all n-dimensions of data in a single file as well as the acquisition settings and other metadata. This file type can only be opened in Nikon's Elements software, the free (but limited) Nikon Elements ND2 Viewer, or in Image J using the ND2 Reader Plugin. If you prefer to process your data using other software, it can be easily exported as a TIFF or other common image formats. It is also possible to capture screen shots by pressing "x" on the keyboard. (Note that 12-bit color images cannot be opened in standard Windows software or MS Office.)

  1. Lumina: Lumina "images" (the picture displayed on the screen in the Living Image software) are saved as a directory of four, 16-bit TIFF images and two text files. Two of the images are "internal" (you never see them on the screen) and are used for normalization. The "photograph" image is the white light photograph seen on the screen, while the "luminescence" image is the image of the luminescent (or fluorescent) signal. These images can be opened in any graphics software that supports 16-bit TIFFs (e.g., ImageJ, Photoshop). While in Living Image, using the "snapshot" command creates an 8-bit PNG of the current view on the screen, which can be opened in virtually any program.
  2. SPECT/CT: After reconstruction, 3D SPECT and CT images are output as 16-bit NIfTI format files (*.nii). This file format can be opened directly in ImageJ or PMOD. From there, the data can be converted to a sequence of many of kinds of 2D image formats, including TIFF. PMOD also supports "screenshots" or movies of the 3D visualizations, which are stored as JPGs.

Data Storage

Upon acquisition, all data is saved within the "Data" folder on the acquisition computer's desktop. Only save data in your folder that is within the main Data folder. Data found in any other location will be deleted immediately and without notice. The facility is not responsible for lost data. Double-click the "Sync Data" icon (located next to the "Data" folder) to upload your data to the PIF FTP site. You may also bring your own portable storage device.

Data Analysis

After acquisition, most images will benefit from additional post-processing. These steps often include adjusting brightness and contrast, removing noise, and picking a color scheme that is most visible to the human eye. Each of these steps must be performed carefully, since they can alter information present in the image or make it less perceptible. The PIF supports a number of imaging processing software packages, whose capabilities are compared here. Users unfamiliar with the proper use of image processing techniques are encouraged to take advantage of our image processing service, especially for images that will be used in publications.

After an image has been processed, it can then be further analyzed using an array of automated quantification routines. For example, objects can be counted, their surface coordinates extracted, co-localization between object computed, etc. 

List of PACUC requirements for live animal imaging

Our approved "Lumina II whole animal imaging" protocol

Our approved "SPECT/CT whole animal imaging" protocol

Technical Information

Comparison of supported image processing programs

IVIS Lumina technical specifications

A1R Confocal technical specifications

A1R MP Multiphoton technical specifications

Invitrogen's Spectra Viewer tool

Free Image Analysis Software

Elements ND2 Viewer


Cell Profiler


More Information

IncuCyte Fluorescent Dye Optimization

mCT Training Request


Nikon A1R MP Training Manual

Nikon A1Rsi Training Manual

Nikon Microscopy Information

Zeiss Confocal Training Manual

Zeiss Microscopy Information