diff --git a/docs/source/INSTALL.md b/docs/source/INSTALL.md index f2374102be439c1e0cfc7beb5eb5f7cacb1d5c21..73ec4b10c28be79e032a60efd83090761094208e 100644 --- a/docs/source/INSTALL.md +++ b/docs/source/INSTALL.md @@ -75,6 +75,37 @@ In case you want to have local version: This will automatically install the [ BABY ](https://git.ecdf.ed.ac.uk/swain-lab/aliby/baby) segmentation software. Support for additional segmentation and tracking algorithms is under development. +## Omero Server + +We use (and recommend) [OMERO](https://www.openmicroscopy.org/omero/) to manage our microscopy database, but ALIBY can process both locally-stored experiments and remote ones hosted on a server. + +### Setting up a server +For testing and development, the easiest way to set up an OMERO server is by +using Docker images. +[The software carpentry](https://software-carpentry.org/) and the [Open + Microscopy Environment](https://www.openmicroscopy.org), have provided +[instructions](https://ome.github.io/training-docker/) to do this. + +The `docker-compose.yml` file can be used to create an OMERO server with an +accompanying PostgreSQL database, and an OMERO web server. +It is described in detail +[here](https://ome.github.io/training-docker/12-dockercompose/). + +Our version of the `docker-compose.yml` has been adapted from the above to +use version 5.6 of OMERO. + +To start these containers (in background): +```shell script +cd pipeline-core +docker-compose up -d +``` +Omit the `-d` to run in foreground. + +To stop them, in the same directory, run: +```shell script +docker-compose stop +``` + ### Troubleshooting Segmentation has been tested on: Mac OSX Mojave, Ubuntu 20.04 and Arch Linux.