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raw2ometiff converter

Java application to convert a directory of tiles to an OME-TIFF pyramid. This is the second half of iSyntax/.mrxs => OME-TIFF conversion.

Requirements

Java 8 or later is required.

libblosc (https://github.com/Blosc/c-blosc) version 1.9.0 or later must be installed separately. The native libraries are not packaged with any relevant jars. See also note in jzarr readme (https://github.com/bcdev/jzarr/blob/master/README.md)

• Mac OSX: brew install c-blosc
• Ubuntu 18.04+: apt-get install libblosc1

Installation

1. Download and unpack a release artifact:

   https://github.com/glencoesoftware/raw2ometiff/releases

Development Installation

1. Clone the repository:

   git clone git@github.com:glencoesoftware/raw2ometiff.git

2. Run the Gradle build as required, a list of available tasks can be found by running:

   ./gradlew tasks

Configuring Logging

Logging is provided using the logback library. The logback.xml file in src/dist/lib/config/ provides a default configuration for the command line tool. In release and snapshot artifacts, logback.xml is in lib/config/. You can configure logging by editing the provided logback.xml or by specifying the path to a different file:

JAVA_OPTS="-Dlogback.configurationFile=/path/to/external/logback.xml" \
raw2ometiff ...

Alternatively you can use the --debug flag, optionally writing the stdout to a file:

raw2ometiff /path/to/zarr-pyramid /path/to/file.ome.tiff --debug > raw2ometiff.log

The --log-level option takes an slf4j logging level for additional simple logging configuration. --log-level DEBUG is equivalent to --debug. For even more verbose logging:

raw2ometiff /path/to/zarr-pyramid /path/to/file.ome.tiff --log-level TRACE

Eclipse Configuration

1. Run the Gradle Eclipse task:

   ./gradlew eclipse

2. Add the logback configuration in src/dist/lib/config/ to your CLASSPATH.

Usage

Run the conversion (Bio-Formats 6.x):

raw2ometiff tile_directory pyramid.ome.tiff

or generate a 5.9.x-compatible pyramid:

raw2ometiff tile_directory pyramid.tiff --legacy

The input tile directory must contain a full pyramid in a Zarr container.

The compression can be changed using the --compression option. Valid compression types are Uncompressed, LZW, JPEG-2000, JPEG-2000 Lossy, JPEG, and zlib. By default, LZW compression will be used in the OME-TIFF file.

If the --compression option is set to JPEG-2000 Lossy, then the --quality option can be used to control encoded bitrate in bits per pixel. The quality is a floating point number and must be greater than 0. A larger number implies less data loss but also larger file size. By default, the quality is set to the largest positive finite value of type double (64 bit floating point). This is equivalent to lossless compression, i.e. setting --compression to JPEG-2000. To see truly lossy compression, the quality should be set to less than the bit depth of the input image (e.g. less than 8 for uint8 data). We recommend experimenting with different quality values between 0.25 and the bit depth of the input image to find an acceptable tradeoff between file size and visual appeal of the converted images.

If the --rgb option is set, the data will be stored in the OME-TIFF using the chunky format and the RGB color space.

Tile compression is performed in parallel. The number of workers can be changed using the --max_workers option.

axes and transformations metadata in the input Zarr will be ignored. This metadata is assumed to be consistent with the corresponding PhysicalSize*, TimeIncrement, and DimensionOrder values in the input METADATA.ome.xml.

License

The converter is distributed under the terms of the GPL license. Please see LICENSE.txt for further details.