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File Format

File format

Image File

The image file store on the computer contains two main things:

  • Image data - pixel values
  • Metadata - Information on your data, such as pixel sizes, objective used, bit depth etc.

It is obvious that image data are important. However, metadata can be of equal importance, for example wrong (or absent) pixel size won't give you any accurate measurement. Therefore, it is crucial to save your data in a format that will preserve the pixel values as well as the metadata.

Note that it is sometime possible to customize the metadata. For example, you could save how the cells were prepared, or the type of antibody you used etc.

Compression

There are two main categories of compression: lossy and lossless.

  1. Lossy compression (e.g. JPEG) saves space by ‘simplifying’ the pixel values, and converting them into a form that can be stored more concisely. But this loses information, since the original values cannot be perfectly reconstructed. It may be fine for photographs if keeping the overall appearance similar is enough, but is terrible for any application in which the exact values matter.

  2. Lossless compression (e.g. PNG, BMP, most types of TIFF) saves space by encoding the patterns in the image more efficiently, but in such a way that the original data can be perfectly reconstructed. No information is lost, but the reductions in file size are usually modest.

Always avoid JPEG!

TIFF is the default format ImageJ use to save data. Most of the software can read this format and almost every acquisition software allow to save files as TIFF. However, in general, not all the metadata will be save in that format, therefore, it is recommanded to always have a copy of your data saved using the company format.

Proprietary format

If you want to be sure you are saving all the metadata with your image file, it usually require to save your data using the particular format of the microscope or acquisition software manufacturer (e.g. ND2 for Nikon, LIF for Leica, OIB or OIF for Olympus, LSM or CZI for Zeiss). And in general, other software can't open this format. Fortunately, the LOCI Bioformats plugin in Fiji, allow to open this type of format. When opening a file using Bioformats, the following dialog box appears first and gives some extra options regarding on how you want the image to be displayed when it is opened.


images


OME-TIFF is the product of an ongoing attempt by the Open Microscopy Environment (OME) to standardize the storage of microscopy images and metadata. See http://www.openmicroscopy.org/.