File Formats in Huygens
Open your microscope files with the Huygens Full File Reader
The Full File Reader option expands Huygens file format compatibility by reading the image data and parameters from proprietary file formats from microscope vendors like Zeiss, Leica, Abberior, Olympus and Nikon. Microscopic Parameters, also known as image metadata, are not only important for generating a correct theoretical PSF for (automated) deconvolution in Huygens, but are also essential for analyzing images properly. For example, the sampling interval values which define the object size in one pixel (voxel) are needed for object size and distance measurements.
For saving your images and to ensure that your metadata is well-preserved, Huygens supports file saving formats known to be very versatile (like for example like HDF5), and that have been developed and highly ranked by the Open Microscopy Environment including ICS and OME-Tiff.
Because of these capabilities, Huygens is ideally suited as a file converter, and since version 20.10, it is also possible to batch convert files easily with the Workflow Processor.
Support for many file formats
The Huygens Software can read many different image file formats.
Microscope file formats
With the Full File Reader option, you can directly open the file formats of your microscope vendor.
Automatic metadata import
Huygens automatically reads as much information as possible concerning the Microscopic Parameters.
Microscopy parameter importHuygens will import as many microscopy parameters as possible from the file headers. You can verify and edit the microscopy parameters in Huygens Microscopy Parameter Editor. In situations when parameters are not present in the metadata or are difficult to read (see difficulties reading metadata), Huygens makes this clearly visible. Colored dots in front of each parameter indicate the status of the parameter value: if you see a green dot the parameter is correct, if you see a blue dot it is nearly correct, with an orange dot the information is not present in the metadata. If the information is missing, Huygens presents default values. We recommend checking orange and blue values before verifying all parameters and proceeding further with image processing, such as deconvolution, visualization and analysis.
The Microscopic Parameter editor in Huygens Essential.
The Microscopic Parameter editor in Huygens Essential.
Loading a image series as a one single multi-dimensional imageFrequently, multi-dimensional (3D-5D and tile) images are stored as a series of numbered images, such as .tiffs. Huygens can read such series within a single directory as one indexed image file. Simply select the first image of the series upon which Huygens automatically searches for patterns in the naming and opens the File Series Tool. Within this File Series Tool you can define for each counter the type of image dimension (Z slice, Channel, Time or Tile). You can always change the image dimensions later using the Convert Tool (see also Convert the dataset). Note that it is recommended to avoid the use of tiff series, as this file format lacks the possibility of storing the metadata information, which is trivial for image analysis.
Opening proprietary file formats with Huygens Full File Reader
Without Full File Reader option
- ICS / ICS2
- OME Tiff (up to 32 bit)
- Multi-layer Tiff
- Leica Tiff series
- Numbered Tiff series
- Olympus Fluoview Tiff
- BigTiff (Uses 64 bit offsets. This allows images larger than 4 GByte)
- Biorad PIC
- Olympus SIS Tiff series
- Delta Vision IMSubs (r3d, dv)
- Imaris Classic version
- Imaris 5.5 HDF5 version
- Huygens Professional only: plain text (csv, txt)
With the Full File Reader option
- Abberior MSR
- Abberior OBF
- 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
- Metamorph STK
- Metamorph ND (version 1.0 and 2.0)
- Nikon ND2 (.nd2)
- Bio Vision IPM (.ipm), IPL (.ipl),IPM (.tif)
File formats the Huygens Software can save
Recommended data types & data conversionWe highly recommend using a file format that is well-supported, preserves the metadata properly, and keeps the information about image dimensions. It is therefore best to save your valuable image data as ICS2, HDF5, or OME Tiff. These recommended formats and other file formats have either 8 bits, 16 bits or 32 bits data types, usually unsigned. There are a few exceptions that use a different format and these are automatically converted in the Huygens software. For example, 12 bit image data is converted to 16 bits when loaded in Huygens. The following table provides a detailed summary:
|8 bit Image||16 bit Image||32 bit Image|
When using recommended formats, the data is saved in the same amount of bits as it is loaded in, e.g., 8 bits as 8 bits. Other file formats are fixed in how many bits they use to store data, which can lead to data loss. This situation is summarized in the following table:
|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.