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TIFF

The TIFF file format is one of the most widely used formats in biosciences. Many commercial instruments write images using some flavor of TIFF. It is used in open source efforts as well; for example, the Open Microscopy Environment developed the OME-TIFF format as an open exchange standard for microscopy data.

ImageJ 1.x support

ImageJ 1.x (and therefore ImageJ2 in its default legacy mode) has built-in support for TIFF files via the FileOpen… command.

You can also import TIFFs as virtual stacks via the FileImportTIFF Virtual Stack… command.

  • Pro: The ImageJ 1.x TIFF reader is very fast.
  • Con: The ImageJ 1.x TIFF support is incomplete. Some valid baseline TIFF files will not open properly. In particular, TIFF files with out-of-order planes cannot be opened.

Bio-Formats

The Bio-Formats plugins offer a more complete TIFF importer, accessible via the FileImportBio-Formats command.

  • Pro: The Bio-Formats TIFF reader can handle many more varieties of TIFF.
  • Con: The Bio-Formats TIFF support is not as speedy as ImageJ1’s TIFF reader.

SCIFIO

The SCIFIO library, the I/O library of ImageJ2, imports TIFF files using code adapted from the Bio-Formats project. As such, it is similar to Bio-Formats in that it supports a wider variety of TIFFs, but is less performant than the ImageJ 1.x reader. SCIFIO is accessible via the FileImportImage… command.

You can tell ImageJ2 to use SCIFIO by default via the EditOptionsImageJ2… menu’s “Use SCIFIO when opening files (BETA!)” checkbox.