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Scientific Volume Imaging B.V.

Scientific Volume Imaging

Deconvolution - Visualization - Analysis




File Formats in ™Huygens

Read your microscopy image and metadata with Huygens Full File Reader 



The Full File Reader option further 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. The 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 correctly measuring object size and distances.
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. Batch file conversion is easily done with the file conversion preset option in Huygens Workflow Processor.


Support for many file formats

The Huygens Software can read many different image formats and dimensions.


Microscope file formats

With the Full File Reader option, you can directly open the file format of your microscope vendor.


Automatic metadata import

Huygens automatically reads as much as possible of the Microscopic Parameters, and presents a useful reliability score of this information.




Microscopy parameter import

Huygens 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.

Selection_211.png
Image description:
The Microscopic Parameter editor in Huygens Essential.

Loading a image series as a one single multi-dimensional image

Frequently, 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




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




Other

  • (Big)TIFF 8 bit & 16 bit & 3*8 bit RGB - Single, multi-layer or File series (Leica Tiff style numbering scheme)
  • Biorad PIC
  • Imaris Classic version
  • Delta Vision IMSubs (r3d) files
  • AVI
  • Huygens Professional only: plain text (csv, txt)
  • Huygens Core only: JPEG (for web applications)


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

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.
tiffScaling.png

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.