Skip to content

Latest commit

 

History

History
140 lines (99 loc) · 6.61 KB

README.md

File metadata and controls

140 lines (99 loc) · 6.61 KB
Raw

3D Slicer / Neuroglancer

Worked on by Julia Thönnißen and Torsten Stöter

Image of the workflow session

Workflow_session

Introduction / Summary

Installing and configuring OMERO

  • We install the OMERO server and web interface using Docker.
  • git clone https://github.com/ome/docker-example-omero
  • follow instructions in README.
cd docker-example-omero/
docker compose pull
docker compose up -d
docker compose logs -f

  • Testing via login to http://localhost:4080 using credentials root / omero

  • Upload some sample images to OMERO via e.g. Insight
    ** 8 bit channels worked well.
    ** 16 bit signed channels did not work out of the box.
    ** The rendering shader in Neuroglancer will need adaption for this.

  • Install omero-web-zarr inside with omero-web Docker container, following instruction at https://pypi.org/project/omero-web-zarr/

docker exec -u 0 -it <omero-web container id> bash
source /opt/omero/web/venv3/bin/activate
pip install omero-web-zarr
  • Commit changes to Docker image and omero-web to new version in docker-compose.yml.
  • Make images in OMERO publically accessible, so that a login on Neuroglancer site is not necessary to fetch the images.
  • Also allow for CORS (Cross Origin Resource Sharing), so that accessing another website from the current one is not blocked
  • Based on https://docs.openmicroscopy.org/omero/5.4.0/sysadmins/public.html, add the following lines in docker-compose.yml under omero-web ENVIRONMENT:
CONFIG_omero_web_public_enabled: true
CONFIG_omero_web_public_user: user-1
CONFIG_omero_web_public_password: 'ome'
CONFIG_omero_web_public_url__filter: '/*'
CONFIG_omero_web_apps: '["omero_figure", "omero_iviewer", "omero_mapr", "omero_parade", "omero_web_zarr", "corsheaders"]'
CONFIG_omero_web_middleware: '[{"index": 1, "class": "django.middleware.common.BrokenLinkEmailsMiddleware"}, {"index": 2, "class": "django.middleware.common.CommonMiddleware"}, {"index": 3, "class": "django.contrib.sessions.middleware.SessionMiddleware"}, {"index": 4, "class": "django.middleware.csrf.CsrfViewMiddleware"}, {"index": 5, "class": "django.contrib.messages.middleware.MessageMiddleware"}, {"index": 6, "class": "django.middleware.clickjacking.XFrameOptionsMiddleware"}, {"index": 0, "class": "whitenoise.middleware.WhiteNoiseMiddleware"}, {"index": 0.5, "class": "corsheaders.middleware.CorsMiddleware"}, {"index": 10, "class": "corsheaders.middleware.CorsPostCsrfMiddleware"}]'
CONFIG_omero_web_cors__origin__allow__all: true
  • OMERO web now exports an image [ID] in zarr publically at the following URL: http://localhost:4080/zarr/v0.4/image/[ID].zarr

Installing Neuroglancer

# install
python3 -m venv neuroglancer-env
source neuroglancer-env/bin/activate
pip3 install neuroglancer

# testing it works
git clone https://github.com/google/neuroglancer
cd neuroglancer/python/examples
python -i example.py
  • For testing, run Neuroglancer in the browser from the provided URL printed at the Python prompt.
  • For our zarr export URL of image ID=63, this script runs the Neuroglancer server (adapted from Neuroglancer tutorial below).
import neuroglancer

ip = 'localhost' #or public IP of the machine for sharable display
port = 9999 #change to an unused port number
neuroglancer.set_server_bind_address(bind_address=ip,bind_port=port)

viewer = neuroglancer.Viewer()

with viewer.txn() as s:
    s.layers['image'] = neuroglancer.ImageLayer(source='zarr://http://localhost:4080/zarr/v0.4/image/63.zarr/')

print(viewer)

Results

  • We successfully could connect OMERO with Neuroglancer and show a proof of concept.

A zarr dataset from OMERO shown in Neuroglancer

  • Technical challenges were all related to access images in omero from external web
  • Login necessary and OMERO cookies not available to Neuroglancer
  • Solution was to grant public access to all routes (NOT RECOMMENDED in production!)
  • HTTP/HTTPS, when using an online version of Neuroglancer with HTTPS, providing an HTTP URL of your local omero-web installation, this unsafe access is blocked
  • Solution was to run OMERO and Neuroglancer both locally and using only HTTP
  • CORS needs to be enabled on OMERO site, when running Neuroglancer and OMERO from different web servers
  • Solution in future can be to run both behind the same webserver, e.g. an nginx reverse proxy each with their own route
  • Another solution would be to build an omero-web plugin for Neuroglancer, possibly right away into omero-web-zarr or as a separate plugin

Report

The final report at the last day of the hackathon for the Neuroglancer topic can be found here.

Outlook

  • Next steps are to get a production ready installation
  • Automate starting the Neuroglancer web server for any image ID
  • Improve shaders for 16bit and multi channel images and include sliders (documented in tutorial)
  • Add an "Open in Neuroglancer" button or context menu to images in OMERO
  • Test the reverse proxy approach, are logins and cookies preserved?
  • Compile a separate OMERO plugin for the Neuroglancer integration