Converting files from FV1000 OIB/OIF to OME-TIFF

This document explains how to convert a file from FV1000 OIB/OIF to OME-TIFF using Bio-Formats version 4.2 and later.

Working example code is provided in FileConvert.java - code from that class is referenced here in part. You will need to have bioformats_package.jar in your Java CLASSPATH in order to compile FileConvert.java.

The first thing that must happen is we must create the object that stores OME-XML metadata. This is done as follows:

ServiceFactory factory = new ServiceFactory();
OMEXMLService service = factory.getInstance(OMEXMLService.class);
IMetadata omexml = service.createOMEXMLMetadata();

The ‘omexml’ object can now be used by both a file format reader and a file format writer for storing and retrieving OME-XML metadata.

Now that have somewhere to put metadata, we need to create a file reader and writer:

ImageReader reader = new ImageReader();
ImageWriter writer = new ImageWriter();

Now we must associate the ‘omexml’ object with the file reader and writer:

reader.setMetadataStore(omexml);
writer.setMetadataRetrieve(omexml);

The reader now knows to store all of the metadata that it parses into ‘omexml’, and the writer knows to retrieve any metadata that it needs from ‘omexml’.

We now tell the reader and writer which files will be read from and written to, respectively:

reader.setId("input-file.oib");
writer.setId("output-file.ome.tiff");

It is critical that the file name given to the writer ends with “.ome.tiff” or “.ome.tif”, as it is the file name extension that determines which format will be written.

Now that everything is set up, we can convert the image data. This is done plane by plane:

for (int series=0; series<reader.getSeriesCount(); series++) {
  reader.setSeries(series);
  writer.setSeries(series);

  byte[] plane = new byte[FormatTools.getPlaneSize(reader)];
  for (int image=0; image<reader.getImageCount(); image++) {
    reader.openBytes(image, plane);
    writer.saveBytes(image, plane);
  }
}

The body of the outer ‘for’ loop may also be replaced with the following:

reader.setSeries(series);
writer.setSeries(series);

for (int image=0; image<reader.getImageCount(); image++) {
  byte[] plane = reader.openBytes(image);
  writer.saveBytes(image, plane);
}

But note that this will be a little slower.

Finally, we must tell the reader and writer that we are finished, so that the input and output files can be properly closed:

reader.close();
writer.close();

There should now be a complete OME-TIFF file at whichever path was specified above.