Simple standalone BigDataViewer for multiple N5 (or HDF5) datasets or mipmap pyramids and also a copy, rechunking, and recompressing tool for N5 and HDF5.

Installation requires maven, OpenJDK8, and lib-hdf5, on Ubuntu:

sudo apt-get install openjdk-8-jdk maven hdf5-tools

On other platforms, please find your way and report back if interested.

Install into your favorite local binary $PATH:

./install $HOME/bin

All dependencies will be downloaded and managed by maven automatically.

This installs two tools, n5-view and n5-copy.

Run the viewer

n5-view \
  -i '/path/file.h5' \
  -i '/path/file.hdf5' \
  -d /volumes/raw \
  -d /prediction \
  -c 0,255 \
  -c -1,1 \
  -r 1,1,10

to look at two datasets or mipmap pyramids from an HDF5 and an N5 container at 1x1x10 resolution and contrast ranges [0,255] and [-1,1]. The viewer maps both contrast ranges into [0,1000] because BDV cannot yet deal with negative intensities and the sliders only show integers. Sorry for the hack.

Copy from N5/HDF5 to N5/HDF5:

n5-copy \
  -i '/path/file.hdf5' \
  -o '/path/file.n5' \
  -b 256,256,26
  -c gzip

or for one or more groups/ datasets:

n5-copy \
  -i '/path/file.hdf5' \
  -o '/path/file.n5' \
  -b 256,256,26
  -c gzip
  -d /volumes

This project can be used to deploy the most useful n5 libraries into an existing Fiji installation where they can be used for scripting. Thanks to the scijava-maven-plugin, you can do this by simply passing your Fiji installation path to maven

mvn -Dimagej.app.directory=$HOME/packages/Fiji.app

Then try the experiments in this script with your own data.