SVI Support Wiki Pages

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 then, even in FreeWare mode) as file converters .

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

Reading

Default Huygens can read the following formats:

• HDF5
• ICS / ICS2
• OME
• TIFF
  • Multi-layer Tiff
  • Leica Tiff series
  • Numbered Tiff series
  • Olympus Fluoview Tiff
• Metamorph STK
• Biorad PIC
• Olympus SIS Tiff series
• MRC
  • Delta Vision IMSubs (r3d, dv)
• Imaris classic
• Huygens Professional only: plain text (csv, txt)

For the following file formats we have a special file reader option available:

• Zeiss ZVI
• Zeiss LSM
• Leica LIF files
• Olympus OIF
• BioVision? IPM (.ipm)
• BioVision? IPM (.tif)

Please note that any index number at the end of a filename will be interpreted by Huygens as plane or time frame number (depending on the file format) in a way that may not be what you intended. It may read all the images in a directory as a single series or stack, when you intended them to be different experiments. Avoid indexes at the very end of the filename that do not stick to the previous conventions. As an easy solution, you can append a text suffix.

See Renaming Tiff Series to match the supported criteria.

Writing

• HDF5
• ICS / ICS2
• OME
• TIFF 8 bit & 16 bit & 3*8 bit RGB - Single, multi-layer or File series ( Leica Tiff style numbering scheme)
• Biorad PIC
• Imaris classic
• Delta Vision IMSubs (r3d) files
• AVI
• Huygens Professional only: plain text (csv, txt)
• Huygens Core only: JPEG (for web applications)

Be careful: writing to TIFF files may alter your data, see Tiff Scaling . JPEG, being a lossy (t.i. not all the original
information is stored to make things smaller) format, is only intended for visualization purposes.

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 .

---