Skip to content
Collaborative volume annotation and segmentation with BigDataViewer
Java Shell
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
data
src
.gitignore
LICENSE
README.md
assignment.json
assignment2.json
bigcat-viewer
install
pom.xml

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

Join the chat at https://gitter.im/saalfeldlab/bigcat Collaborative volume annotation and segmentation with BigDataViewer

You can’t perform that action at this time.