OMERO-3Dscript 0.0.10

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

OMERO.3Dscript

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

Enabling the public user

If you want to grant the 'public user' the permission to render 3D animations using 3Dscript, you need to enable it as described here:

omero config set omero.web.public.enabled True
omero config set omero.web.public.user '<username>'
omero config set omero.web.public.password '<password>'
omero config set omero.web.public.url_filter '^/(webadmin/myphoto/|webclient/(?!(script_ui|ome_tiff|figure_script))|webgateway/(?!(archived_files|download_as))|iviewer|api|3Dscript)'
omero config set omero.web.public.get_only false

Pay attention to the last two lines.

See also

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

Publication

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

Schmid B., Tripal P., Winter Z. & Palmisano R. (2021), "3Dscript.server: true server-side 3D animation of microscopy images using a natural language-based syntax", Bioinformatics 37(24): 4901-4902, PMID 34152405.