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.