Scientific Volume Imaging

The Olympus VSI file format is a container which can hold various types of files.

So the user of CellSense can choose which method to apply on the images.

Then it is good to know that Huygens reads the following VSI types::

• the ets files with raw uncompressed data
• the ets files with uncompressed Tifs
• the ets files with uncompressed Jpegs (lossless)

The only Olympus VSI type that Huygens cannot read is:

• the ets Tifs which are compressed with JPEG

In short, do not compress your VSI data if you want to deconvolve them because the loss of data that most compression entails is very counter-productive to deconvolution.

Note: For VSI files with .ets files included the compression format is mentioned in the metadata:

• raw (no compression)
• jpeg
• j2k (jpeg2000)
• png
• bmp

Here you will also see the compression quality mentioned. If the compression quality is not 100% (lossless compression) Huygens will give a warning that compression with data loss was used and will not proceed.

VSI/ETS issues

If you encounter issues with reading ETS files accompanied with your VSI file, make sure that the folder containing the ETS files is not renamed.

Usually these files will have the following naming convention:

• filename.vsi (VSI file)
• _filename_ (directory)*
  • stack1 (sub-directory)
    • frame_t_0.ets (ETS file)

*The underscore (_) character in this directory with the same filename as the VSI are important