File formats

There is a tremendous amount of image file formats (see Wikipedia: Image file formats) and multidimensional images are no exception with more than 150 formats known to bio-formats (see their documentation).

Supported formats

For now, we make use of the IO library from VT (Morpheme INRIA Team), thus timagetk accept the following formats:

  • INR: allegedly an INRIA image format, no documentation available online. Should probably be considered as DEPRECATED! See: bio-formats: INR

  • TIFF: Tagged Image File Format, also abbreviated TIF, is a computer file format for storing raster graphics images, see Wikipedia: TIFF

  • MHA: no documentation available online, unsupported by bio-format. Should probably be considered as DEPRECATED!

  • LSM: See: bio-formats: Zeiss LSM

Although they are quite common formats, especially TIFF & LSM, these are very limited options and most of them only work with 2D or 3D images at best.

Unsupported formats

There should be an effort to be able to handle more than these 4 file formats, notably to support CZI files that allows to save multidimensional images with more than 3 dimensions. Supporting the

Notes

OME & OME-XML formats from Omero also appears as a good idea!

CZI file can be read using a third party library.