OMERO-NB-index - An OMERO plugin for connecting Nucleome Browser with OMERO

Introduction

OMERO-NB-index (formerly known as omero2cnb) allows users to interactively explore imaging datasets stored on a local OMERO server in a genome browser panel of Nucleome Browser. OMERO server uses a PostgreSQL database to store the annotation information of images. OMERO-NB-index extracts and monitors the key-value map stored in the annotation_mapvalue table in PostgreSQL database. If a key is named as regions, and the format of value follows genome:chromosome:start-end;... , such as hg38:chr1:1-20000;hg38:chr1:30000-40000, OMERO-NB-index will parse these values into genome coordinates and store them into a binning index data structure and create a web service at http://127.0.0.1:3721. Use then can add this web service in the genome browser of Nucleome Browser, and query images based genomic coordinates through the navigation on the genome browser. By default, OMERO-NB-index monitors the change of annotation_mapvalue table every 90 seconds.

If you want to use this web service other than a local OMERO server, please use reverse proxy software such nginx or traefik.

Install

go get github.com/nucleome/omero2cnb

Usage

omero2cnb [db_host] [dbname] [db_user] [db_passwd] [omero_web_server]

Docker

• OMERO-NB-index in Docker Hub
• Dockerfile in GitHub This docker file requires a binary executable file. You can generate it using the following command.

git clone https://github.com/nucleome/omero2cnb
cd omero2cnb
env CGO_ENABLED=0 GOARCH=amd64 GOOS=linux go build

Docker Compose with OMERO

User can start a docker compose along with OMERO and OMERO.web.

• Docker compose file