OMERO-3Dscript 0.0.5

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 for the server:

• OpenCL capable graphics card
• Updated graphics 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 add-update-site 3Dscript-server "https://romulus.oice.uni-erlangen.de/imagej/updatesites/3Dscript-server/"
    ./ImageJ-linux64 --update update
    apt-get update && apt-get install -y -qq ffmpeg > /dev/null

• Install OMERO.3Dscript

    pip install omero-3Dscript

• Tell OMERO.3Dscript where to find Fiji

    omero config set omero.web.omero_3Dscript.fiji_bin "/usr/local/share/Fiji.app/ImageJ-linux64"

:warning: On Mac OS X, you need to replace ImageJ-linux64 with Contents/MacOS/ImageJ-macosx

• 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

See also:

• https://github.com/bene51/3Dscript
• https://github.com/bene51/3Dscript.server

Publication:

Schmid, B.; Tripal, P. & Fraass, T. et al. (2019), "3Dscript: animating 3D/4D microscopy data using a natural-language-based syntax", Nature methods 16(4): 278-280, PMID 30886414.