SCIFIO is a flexible framework for SCientific Image Format Input and Output. In other words, it is a library for reading and writing N-dimensional image data—e.g., to and from files on disk. SCIFIO is built on the SciJava Common library.
ImageJ2 uses SCIFIO by default for most image input tasks. You can change this behavior at any time by running Edit › Options › ImageJ2 and modifying the Use SCIFIO when opening files option.
Benefits of using SCIFIO
SCIFIO is focused on robust and extensible support for reading and writing image file formats. Using it with ImageJ provides many advantages:
- There is no need to call a special SCIFIO plugin; it works with commands like File › Open automatically.
- There are additional import options available via the File › Import › Image… command.
- There is a Bio-Formats plugin for SCIFIO, included with the Fiji distribution of ImageJ, that adds automatic support for over a hundred life sciences file formats.
- Additional SCIFIO file format plugins can be dropped into ImageJ and will also work automatically.
- Unlike the ImageJ 1.x TIFF implementation, SCIFIO’s support for TIFF adheres to the specification, allowing to successfully read many more sorts of TIFFs.
- Similarly, SCIFIO supports more sorts of JPEG files since it uses its own JPEG decoder.
- SCIFIO also ships with support for several QuickTime codecs, allowing ImageJ to read QuickTime MOV files even in 64-bit mode without QuickTime for Java.
- SCIFIO supports many additional open file formats out of the box:
- animated GIF
- animated PNG
- encapsulated postscript (EPS)
- Micro-Manager datasets
- Multi-image Network Graphics (MNG)
- Nearly Raw Raster Data (NRRD)
- Imspector OBF
- OME-TIFF (multidimensional rich metadata TIFF)
- PICT (even in 64-bit mode and/or without QuickTime for Java installed)
- If SCIFIO cannot handle the image file, it falls back to ImageJ 1.x.
- You can save to SCIFIO-supported file formats using the File › Export › Image…
command. Supported formats for export include:
Current limitations of SCIFIO
- SCIFIO is still in beta, so there is likely to be a higher incidence of bugs. Issues can be reported on the SCIFIO issue tracker.
- Although we strive for full backwards compatibility, some files may appear slightly different when opened.
- Opening files with SCIFIO is not fully macro recordable yet.
Hiner, M.C.; Rueden, C.T. & Eliceiri, K.W. (2016 Dec 7), “SCIFIO: an extensible framework to support scientific image formats.”, BMC Bioinformatics 17(1): 521, PMID 27927161, doi:10.1186/s12859-016-1383-0 (on Google Scholar).