saalfeldlab / bigcat

Collaborative volume annotation and segmentation with BigDataViewer

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