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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.

(In the following lists some items have further explanations, but all of them are supported).

Reading

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

With the additional Full File Reader License Option Huygens can also read the below file formats:

  • Zeiss CZI
  • Zeiss ZVI
  • Zeiss LSM
  • Leica LIF files
    • LAS AF format version 2 and 3.
  • Olympus OIF (VSI expected December 2014)
  • Bio Vision IPM (.ipm)
  • Bio Vision IPL (.ipl)
  • Bio Vision IPM (.tif)
  • Metamorph STK
  • Nikon ND2 (.nd2)

After opening an image the Huygens software will set the image data type to 32 bits, 16 bits or 8 bits (1 byte), depending on the source file data type. The following situations may occur:
  • The file data type is 32 bits: Huygens will import the data as 32 bits.
  • The file data type is 16 bits: Huygens will typically ask whether to convert it to 8 bits, 32 bits or just leave it as 16 bits.
  • The file data type is 8 bits: Huygens will import the data as 8 bits.


The following table summarizes how these three situations apply to each file format. Rows with more than one data type show that Huygens will prompt for a data type choice:

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 Image Image
tiff 8 bit Image
tiff-rgb 8 bit Image
lsm 12 bit Image
lsm 8 bit Image
pic 16 bit Image Image Image
pic 8 bit Image
r3d 32 bit Image
ims 8 bit Image
ome 32 bit Image
zvi 16 bit Image Image 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



When opening a file notice that index numbers at the end of a filename are interpreted by Huygens as a slice or time frame number (depending on the file format). Huygens can read all the images in a directory as a single series or stack. Please avoid indexes at the end of filenames that do not stick to the previous conventions. See Renaming Tiff Series to match the supported criteria.

Saving


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).

It is always recommended to verify the Microscopic Parameters after reading a file.

Other information

See also Joining Channels.

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