imaris-writer

Java code for saving 3D multi-channel movies into a multi-resolution Imaris compatible hdf5 format.

Imaris file format

See here for Imaris file format specifications: http://open.bitplane.com/Default.aspx?tabid=268

Input formats

Supported input image formats are:

• ImagePlus objects, as they are used in ImageJ.

File format

An example output, for the filename image looks like this:

• image-header.ims
  • an hdf5 file, linking into below volumes
• image--C00--T00000.h5
  • hdf5 file containing multiple resolution levels
• image--C01--T00000.h5
  • hdf5 file containing multiple resolution levels
• image--C00--T00001.h5
  • hdf5 file containing multiple resolution levels
• image--C01--T00001.h5
  • hdf5 file containing multiple resolution levels

High-level reading options

Imaris

The *.ims header file be opened using Imaris.

BigDataViewer

The *.ims header file can be opened within Fiji:

• [ Plugins > BigDataViewer > Open Imaris (experimental) ]

Example java code that achieves the same:

import bdv.spimdata.XmlIoSpimDataMinimal;
SpimDataMinimal image = new XmlIoSpimDataMinimal().load( file.getAbsolutePath() );
BdvFunctions.show( image );

BigDataConverter

Individual resolution levels can be lazy-loaded using:

• [ Plugins > BigDataTools > BigDataConverter ]

which will open them as a 5D VirtualStack, i.e. a lazy-loading data structure feeding pixel values into an ImagePlus.

BigDataConverter2

Individual resolution levels can be opened using

• [ Plugins > BigDataTools > BigDataConverter2 ]

which will open them as a 5D CachedCellImage, i.e. a lazy-loading data structure feeding pixel values in a RandomAccessibleInterval.

Technical details

Hdf5 library

<dependency>
    <groupId>cisd</groupId>
    <artifactId>jhdf5</artifactId>
</dependency>

import hdf.hdf5lib.*

As far as we know, this is the most core hdf5 library and should contain all functionality. We also explored the higher level ch.systemsx.cisd.hdf5 library, but certain functionality, such as filters did not seem to be available.

Future plans

• Create per channel sub-folders