Free online VSI to OME.TIFF converter

What the VSI format is

VSI is a proprietary virtual-slide format used by Olympus VS-series scanners and Olympus cellSens software. A VSI dataset can contain tiled, multi-resolution microscope images, multiple channels, multiple focal planes, and acquisition metadata. It is usually encountered with a companion folder containing image data, so copy the entire original dataset before conversion; moving only the .vsi file can make the slide unreadable.

What the OME-TIFF format is

OME-TIFF is a TIFF-based microscopy format that stores pixels together with OME-XML metadata describing dimensions, channels, planes, physical pixel sizes, and related acquisition information. It is supported by Fiji, Bio-Formats, QuPath, napari with suitable plugins, and many scientific image-processing libraries.

OME-TIFF is preferable when software cannot read VSI, when datasets must be exchanged between microscopy applications, or when metadata needs to remain in a documented structure. It can use lossless compression such as LZW and can be written as BigTIFF when the output exceeds the classic TIFF size limit.

How to convert VSI to OME-TIFF

Using Bio-Formats

Bio-Formats is the most direct desktop and command-line option because it includes a VSI reader and an OME-TIFF writer.

1. Install Fiji, which includes Bio-Formats, or download the Bio-Formats command-line tools.
2. Keep the .vsi file and its associated data folder together.
3. For a command-line conversion, run:

bfconvert -compression LZW -overwrite input.vsi output.ome.tiff

Use BigTIFF for a very large result:

bfconvert -bigtiff -compression LZW -overwrite input.vsi output.ome.tiff

If the VSI contains several image series, inspect the series list first and convert the required series separately. Bio-Formats may otherwise write multiple series or produce output names based on the source series. A typical series-specific command is:

bfconvert -series 0 -compression LZW -overwrite input.vsi output-series-0.ome.tiff

The exact available options depend on the Bio-Formats version; run bfconvert -help to verify them.

Using Fiji

1. Open the dataset through Plugins → Bio-Formats → Bio-Formats Importer.
2. Select the VSI file and preserve the original dimensions, channels, and series in the importer options.
3. Export the opened image through File → Save As → OME-TIFF, or use the Bio-Formats exporter where available.
4. Select LZW compression for lossless storage and choose BigTIFF if the estimated output is larger than 4 GB.

For a whole-slide image, verify whether the selected exporter preserves a multi-resolution pyramid. If it exports only the currently opened resolution, the result is a valid OME-TIFF but not an equivalent pyramidal slide.

Converting without installed software

You can convert the file on the 101convert.com website for free without installing software, provided the service accepts the VSI dataset and its associated files. Upload the complete dataset when the converter requests companion files, and confirm that the resulting OME-TIFF contains the required series and metadata.

Quality, compatibility, and limitations

LZW compression is lossless, so it preserves pixel values while reducing size; JPEG compression can introduce artifacts and is unsuitable when quantitative measurements depend on the original pixels. A conversion cannot restore information absent from the VSI reader or exporter, and some Olympus-specific annotations, stage data, pyramid details, or proprietary metadata may not map to OME-XML.

Check the output in Fiji or Bio-Formats by comparing width, height, channel count, z-depth, time points, pixel type, and physical pixel size with the source. Also test the file in the target application: a standards-compliant OME-TIFF may contain valid metadata yet lack the pyramidal layout or vendor-specific annotations required by a particular whole-slide viewer.