Introduction to Bio-Formats

...and in many different applications

Java:
ImageReader reader = new ImageReader();
IMetadata omeMetadata = MetadataTools.createOMEXMLMetadata();
reader.setMetadataStore(omeMetadata);
reader.setId("/PATH/TO/FILE");
for (int plane = 0; plane < reader.getImageCount(); plane++) {
  byte[] image = reader.openBytes(plane);
  Number timestamp = omeMetadata.getPlaneDeltaT(0, plane).value();
}

                

ImageJ macro:
run("Bio-Formats Macro Extensions");
Ext.setId("/PATH/TO/FILE");
Ext.getImageCount(imageCount);
timestamps = newArray(imageCount);
for (plane=0; plane < imageCount; plane++) {
  Ext.openImage("image #" + plane, plane);
  Ext.getPlaneTimingDeltaT(timestamps[plane], plane);
}
                

MATLAB:
r = bfGetReader("/PATH/TO/FILE");
imageCount = r.getImageCount();
omeMetadata = r.getMetadataStore();
for plane = 1:imageCount
  image = bfGetPlane(r, plane, varargin{:});
  timestamp = omeMetadata.getPlaneDeltaT(0, plane - 1).value().doubleValue();
end
                

Python:
reader = bioformats.get_image_reader(None, path="/PATH/TO/FILE")
imageCount = reader.rdr.getImageCount()
omeMetadata = javabridge.JWrapper(reader.rdr.getMetadataStore())
for plane in range(0, imageCount):
    image = reader.read(series=0, index=plane, rescale=False)
    timestamp = omeMetadata.getPlaneDeltaT(0, plane)
                

R:
reader = .jnew("loci.formats.ImageReader")
.jcall(reader, , "setId", file)
omeMetadata = .jcall(reader, "", "getMetadataStore")
image = .jcall(reader, "[B", "openBytes", 0)
timestamp = .jcall(omeMetadata, "", "getPlaneDeltaT", 0, 0)
                

Extensions to image reading

• cache reader state (Memoizer)
• group independent files into a single dataset (FileStitcher)
• return images in a specific layout (ChannelSeparator, ChannelMerger)

Memoizer

IFormatReader reader = new Memoizer(new ImageReader());
reader.setId("/PATH/TO/FILE");
                    

• uses Kryo to serialize the reader's initialized state to a file
• initializing the same data file again uses the serialized state (i.e. faster)

FileStitcher

IFormatReader reader = new FileStitcher();
// reads 001.tiff, 002.tiff, ..., 010.tiff together
reader.setId("0< 01-10>.tiff");
                    

• groups together files not otherwise detected as part of the same dataset
• useful for files with missing or unreadable metadata

ChannelSeparator/ChannelMerger

IFormatReader grayscaleImageReader = new ChannelSeparator();

IFormatReader rgbImageReader = new ChannelMerger();
                    

• ChannelSeparator guarantees only grayscale images are returned
• ChannelMerger guarantees multi-channel datasets are returned as RGB images

Putting everything together...

IFormatReader reader = new Memoizer(new FileStitcher(new ChannelSeparator()));
                  

• any combination of wrappers can be chained together

What we've done recently

• maintenance of 5.1.x
• 5.2.0
• performance and metadata updates for IDR

Bio-Formats 5.1.x series

See the Bio-Formats version history

• Reader bug fixes
• Support for native units across readers
• OMERO / Bio-Formats decoupling
• Documentation improvements

Bio-Formats 5.1.x series: community

See the Bio-Formats version history

• Readers (Metamorph, Slidebook, Fei, Imspector OBF)
• MATLAB toolbox
• Octave package
• OME-XML validation

Bio-Formats 5.2.0

Breaking changes

• New OME Data model
• Code generation improvements
• Drop of support for Java 6
• API (logging)

Bio-Formats IDR

• Lots of performance improvements for HCS formats
• Improved support for different types of Opera Flex plates
• More options for grouping together files without acquisition metadata