SVI encourages the use of open-source file formats that contain image metadata. We recommend to use ICS2, ICS, OME or HDF5.

Huygens supports many common microscopy file formats. For closed-sourced (non-documented) file formats the Full-File Reader option is required. On our File Formats page you can find a complete overview.

TIFF images come in many different varieties. Currently Huygens only supports strip TIFF files (files in which the data is written in on strip), which is by far the most common form of TIFF. By default Huygens will read in multiple strips as Z-slices. If this is incorrect you can easily correct for this using the convert tool (see "How can I fix images that have been opened incorrectly?").

Huygens will automatically recognize files that are named similarly with a counter for tiles, z-slices and channels if they are in the same order. If you open one image that is part of the series the Huygens File Series Tool will be opened in which you configure the file opening manually. See also our TIFF webpage for more details.

Although Huygens can open many different file formats without any issues it sometimes happens that certain TIFF formats are not read in properly. However, as long as all the intensities are read in it is usually possible to correct the image. For misreadings of the Channels, time-frames or Z-slices you can use or convert tool in the "Tools" menu or in the Workflow Processor for batch processing. If not all intensities are read in you can best contact support (support@svi.nl) or try to convert it to a supported file format (see also our File Formats page). If the metadata is read incorrectly you can also easily fix this in Huygens. Simply select the faulty image and open the microscopic parameter window (right-click menu or notepad icon). After setting the microscopic parameters correctly you can save them as a template so you can easily use the same parameters for other images.

The three modes: Contrast stretch, linked scale and clipped determine the way data is scaled if the intensity range of the image is bigger than what can be saved in the TIFF file. Each of the scaling methods has its own pro's and cons. Details on the different methods can be found on our TIFF webpage.

Imaris can open the ICS file format. Old versions of Imaris also can open the classic imaris file format from Huygens.

Huygens reads the Imaris HDF5 format.