Command-line tool and library for converting bioimaging filesets into the SpaceTx format. Generated filesets contain the required SpaceTx metadata in JSON, 2D TIFF stacks, and an OME companion file.
The following are required:
JDK 7 or higher
Gradle
From the root directory, run:
gradle build
Downloaded files (including the Gradle distribution itself) will be stored in
the Gradle user home directory (~/.gradle by default).
You will need to unpack one of the built distribution from build/distributions, e.g.:
unzip -d /tmp/ build/distributions/spacetx-writer-$VERSION.zip
/tmp/spacetx-writer-$VERSION/bin/spacetx-writer
If instead of installing a JDK and building from source, you can locally build the docker image: From the root directory, run:
docker build -t spacetx-writer .
Running the built image will call the spacetx-writer executable by default.
Finally, you can pull a pre-built image from Docker Hub:
docker pull spacetx/spacetx-writer
If you would like to use the docker image, it is important that you mount input and output directories into the container:
docker run -ti --rm -v /tmp:/tmp -v /data:/data:ro spacetx-writer ...
Once that is done, behavior of the docker container and the command-line are the same. A simplest invocation would be:
spacetx-writer -o /tmp/new-directory /data/my-data.nd2
See -h for more information.
Bio-Formats takes a single input file, searches through around 150 different file formats to determine the type, and then groups associated files together into a single fileset automatically. You can see a list of the file formats and which file should be chosen on the Datset Structure Table page.
If Bio-Formats does not detect the data type, you may need to tell it how to group multiple multiple unrelated files into a single fileset. This can be done by creating a "pattern file".
For example, if you have 5 large TIFF files t1.tif through t5.tif, each representing a separate round, create a file with the contents:
t<1-5>.tif
and pass it to the tool. Similarly, if you have several 2D TIFFs, create a file which matches your chosen pattern:
my_tiffs_z<1-12>_c<1-3>_t<1-100>.tiff
For more information, see the Grouping files using a pattern file page on the Bio-Formats documentation.
If you pass multiple files to the tool, they will be interpreted as separate filesets, each of which which will be made into a field-of-view. The FOV will have the dimensions detected by Bio-Formats. If Bio-Formats does not show the expected dimensions, you may need to try grouping files.