OMERO-3Dscript 0.0.1

OMERO.web app to animate multi-dimensional microscopy using 3Dscript, directly from within the OMERO environment.

Usage:

• Open OMERO.web in the browser
• Open OMERO.3Dscript:
  • by clicking on '3Dscript' on the top links
  • right-click an image in the explorer and select 'Open with' -> '3Dscript'
• Enter the animation text (see https://bene51.github.io/3Dscript/ for more details)
• Click on 'Render'

Requirements:

• OpenCL capable graphics card
• Updated drivers

Installation:

OMERO.3Dscript needs to be installed on the machine that runs OMERO.web.

• Install Fiji and the 3Dscript and 3Dscript.server plugins.

    FIJI_HOME=/usr/local/share/Fiji.app
    mkdir $FIJI_HOME
    cd `dirname $FIJI_HOME`
    wget https://downloads.imagej.net/fiji/latest/fiji-linux64.zip
    unzip fiji-linux64.zip
    cd Fiji.app
    ./ImageJ-linux64 --update add-update-site 3Dscript https://romulus.oice.uni-erlangen.de/updatesite/
    ./ImageJ-linux64 --update update
    apt-get update && apt-get install -y -qq ffmpeg git vim > /dev/null
    cd $FIJI_HOME/jars
    wget -q https://github.com/ome/omero-insight/releases/download/v5.5.9/omero_ij-5.5.9-all.jar
    cd $FIJI_HOME/plugins
    wget -q https://bitbucket.org/bene51/omero_3dscript/downloads/3D_Animation_Server-0.1.jar

• Install OMERO.3Dscript

    install_dir=`pip show omero-web | grep Location | cut -d' ' -f 2` # find out where OMERO.web is installed
    cd $install_dir
    git clone https://github.com/bene51/omero_3Dscript.git
    pip install pid

• Add it to the OMERO.web UI:

    omero config append omero.web.apps '"omero_3Dscript"'
    omero config append omero.web.ui.top_links '["3Dscript", "3Dscript_index", {"title": "Open 3Dscript in a new tab", "target": "_blank"}]'
    omero config append omero.web.open_with '["3Dscript", "3Dscript_index", {"supported_objects": ["image"], "target": "_blank", "label": "3Dscript"}]'

• Restart OMERO.web as normal