README.md

BIGCAT (working title)

Install

Install Script

The install script uses Maven to download and manage dependencies, compiles and installs BigCAT into the local Maven repository, and installs a start-script bigcat (tested on Linux and MacOS only, but can be reproduced on Windows with some manual tweaking).

./install $HOME/bin

Run the installed start-script

bigcat -i  <input_hdf_file> -l <label/dataset> -r <raw/dataset>

Conda

BigCAT is available on conda:

conda install -c hanslovsky bigcat

Run instructions missing...

Fat JAR

To compile a "fat jar" with all dependencies included, run:

mvn clean compile assembly:single

Run it

java -Xmx16G -jar target/bigcat-<VERSION>-jar-with-dependencies.jar -i <input_hdf_file> -l <label/dataset> -r <raw/dataset>

Documentation

Documentation is on the Wiki.

Development

Collaborative volume annotation and segmentation with BigDataViewer