File formats

The Huygens Software is capable of reading and writing different microscopy image file formats.

Because of these capabilities, you can use the packages in the Huygens Suite (for many of them, even in freeware mode) as file converters.

You are welcome to explore the Full File Reader option and all other options of Huygens by downloading our software and requesting a free trial license. Of course you are also more than welcome to ask for pricing information!


In basic mode the Huygens software can read the following file formats:

With the additional Full File Reader Option Huygens can also read:

  • Zeiss CZI
  • Zeiss ZVI
  • Zeiss LSM
  • Leica LIF files
    • LAS AF format version 2 and 3.
  • Leica LOF
  • Leica XLIF
  • Olympus OIF
  • Olympus VSI
  • Olympus OIR (New)
  • Metamorph STK
  • Metamorph ND (version 1.0 and 2.0)
  • Nikon ND2 (.nd2)
  • Bio Vision IPM (.ipm), IPL (.ipl),IPM (.tif)

Basic pixel data types

Most microscopic file formats contain either 8bit or 16bit unsigned pixel data, but there are exceptions. The following table summarizes how the file pixel data is handled in Huygens:

8 bit Image 16 bit Image 32 bit Image
ics 32 bit Image
ics 16 bit Image
ics 8 bit Image
ics2 32 bit Image
hdf5 32 bit Image
tiff 16 bit Image
tiff 8 bit Image
tiff-rgb 8 bit Image
lsm 12 bit Image
lsm 8 bit Image
pic 16 bit Image
pic 8 bit Image
r3d 32 bit Image
ims 8 bit Image
ome 32 bit Image
zvi 16 bit Image
stk 16 bit Image
mrc 32 bit Image
ipl 16 bit Image
ipm 8 bit Image
seq 16 bit Image
lif 16 bit Image
lif 8 bit Image
oif 16 bit Image
nd2 16 bit Image

Indexed file names

Index suffixes at the end of a filename are interpreted by Huygens as an XY slice or time frame number (depending on the file format). Huygens can read a series of indexed image files contained in a single directory as one 3D of 4D image. Please avoid indexes at the end of filenames that do not stick to the supported conventions. See renaming Tiff series for the supported criteria.


Depending on the file format chosen to save the image the file data type will be 32 bits, 16 bits or 8 bits. The image, as read by Huygens, has either 32 bits, 16 bits or 8 bits as data type. This presents a number of combinations from the data types of the open image to data types of the saved image. This situation is summarized in the following table, where the cells show the data type of the resulting file given a source image and a destination file format:

hdf5 ics ics2 tiff 8 tiff 16 tiff-rgb imaris biorad 8 biorad 16 ome-xml delta r3d
8 bit Image 8 bit 8 bit 8 bit 8 bit 16 bit 8 bit 8 bit 8 bit - 8 bit 8 bit
16 bit Image 16 bit 16 bit 16 bit 8 bit 16 bit 8 bit 8 bit 8 bit 16 bit 16 bit 16 bit
32 bit Image 32 bit 32 bit 32 bit 8 bit 16 bit 8 bit 8 bit 8 bit 16 bit 32 bit 32 bit

When the chosen file extension implies fewer bits than those of the image, for example saving a 32 bit image to a 16 bit file, the software will prompt for a conversion method choice: Contrast stretch, Linked stretch or clipping.

Please note that writing to TIFF files may alter the data, see Tiff scaling. JPEG, being a lossy format, i.e. not all the original information is saved, is only intended for visualization purposes and is therefore not listed in the above table.

Metadata import

The software will try to import from the file headers as much information as possible concerning the Microscopic Parameters. This is not always feasible: some formats do not store this information at all, other store it in a way that is difficult to read (see difficulties reading metadata). Huygens made that all directly visible: if you see a green dot all meta data are correct, if you see a blue dot it is nearly correct, with an orange dot there was no information in the metadata at all, Huygens then uses the default ranges for those kind of images. We recommend to check orange and blue values before proceeding with the deconvolution.
If the metadata of a hyperstack image with z stacks of multiple positions is not read by Huygens, it is recommended to save the individual stacks as ics/ids for Huygens.

It is always recommended to verify the microscopic parameters after reading a file.

Other information

See also Joining Channels.

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Contact Information

Scientific Volume Imaging B.V.

Laapersveld 63
1213 VB Hilversum
The Netherlands

Phone: +31 (0)35 64216 26
Fax: +31 (0)35 683 7971
E-mail: info at svi.nl

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