OME-CATMAID

Using CATMAID to visualize images stored in OMERO server.

CATMAID is a well-known annotation application for large scale bioimages, particularly for neuronal images. CATMAID itself does not host any images. On the other hand, OMERO is a full environment for bioimages storage and manangement. It supports various APIs to work with many languages. Linking CATMAID and OMERO allows us to profit the advantages of the both two apps.

Installation

We suppose that you installed OMERO and CATMAID. Here are the steps to link these two apps.

OMERO side

Download omero-catmaid folder and add its directory into PYTHONPATH

$ export PYTHONPATH=$PYTHONPATH:/path/to/omero-catmaid-folder

then, add omero-catmaid app to OMERO.web

$ OMERO.py/bin/omero config append omero.web.apps '"omero_catmaid"'

and restart OMERO web.

$ OMERO.py/bin/omero web restart

CATMAID side

Define new tile source type in catmaid/django/applications/catmaid/static/js/tile-source.js

CATMAID.OmeroTileSource = function(baseURL, fileExtension, tileWidth, tileHeight) {
  this.getTileURL = function( project, stack, slicePixelPosition, col, row, zoomLevel ) {
    return baseURL + '&' + $.param({
      z : slicePixelPosition[0],
      t : 0,
      x: col * (tileWidth*(2**zoomLevel)),
      y: row * (tileHeight*(2**zoomLevel)),
      w : tileWidth,
      h : tileHeight,
      zm : zoomLevel
    });
  };

  this.getOverviewLayer = function( layer ) {
    return new CATMAID.ArtificialOverviewLayer(layer);
  };
};

then find the tileSources definition in tile-source.js and add a new tile source in tileSources list

var tileSources = {
      '1': CATMAID.DefaultTileSource,
      …
     ‘10’: CATMAID.OmeroTileSource
};

The next step is to add the new tile source in catmaid/django/applications/catmaid/models.py

# Supported tile source types
TILE_SOURCE_TYPES = (
    (1, '1: File-based image stack'),
    …
    (10, '10: OmeroServer tiles')

and run the following commands to update the change

./manage.py makemigrations
./manage.py migrate
./manage.py collectstatic -l # re-run when modify tile-source.js
./run-gevent.py