The Next Generation Embryology Project aimed to develop a web application which provides annotations over 3D rendering of embryos.
The following are videos of ngembryo in use. They were created by Rosa Spencer of Newcastle University. I plan to update these videos with the latest resources made available recently at the eMouse Atlas web portal.
- Quick demonstration of the ngembryo portal
- How to add a new marker and link a resource
- How to create a new orientation, layer, marker and region
For now, I will describe the process to get this running under Mac OSX. This project uses Apache web server and MySQL database server, which come already installed in Mac OSX. If not, please Google for installation instructions.
Enable PHP, by uncommenting PHP5 module (
LoadModule php5_module libexec/apache2/libphp5.so).
$ sudo vi /etc/apache2/httpd.conf
Ensure that MySQL server is accessible to PHP.
$ sudo cd /var $ sudo mkdir mysql $ sudo ln -s /tmp/mysql.sock /var/mysql/mysql.sock
We will use the user's
Sitesdirectory to deploy
ngembryo. Create the
Sitesdirectory if it does not exists.
$ whoami user $ cd ~ $ mkdir Sites
Download the source code:
$ cd Sites $ git clone https://github/gyaikhom/ngembryo.git $ cd ngembryo
Install the database, and check that it is accessible to user
$ pwd /Users/user/Sites/ngembryo $ cd resources $ mysql -u root < ngembryo.sql
Since the embryo images are hosted at MRC Edinburgh, we will have to set up a proxy so that request for images are re-directed.
$ sudo vi /etc/apache2/other/proxy.conf
Add the following:
<IfModule mod_proxy.c> ProxyRequests On ProxyPreserveHost On ProxyStatus On <Location /status> SetHandler server-status Order Deny,Allow Deny from all Allow from 127.0.0.1 </Location> ProxyPass /fcgi-bin/iip3dsrv_ema.fcgi http://www.emouseatlas.org/fcgi-bin/iip3dsrv_ema.fcgi ProxyPassReverse /fcgi-bin/iip3dsrv_ema.fcgi http://www.emouseatlas.org/fcgi-bin/iip3dsrv_ema.fcgi </IfModule>
Start apache server
$ sudo apachectl start
http://localhost:80/~user/ngembryo. Register as user, and
ngembryois ready for use.
This project was funded by JISC to develop a
prototype system. The project was funded for 18 months. Design began in
September 2009, and active development started in January 2010. The project
has now concluded, and as of 1 October, development has also ceased. Further
details are in the
I am releasing the source code here, so that it is accessible to embryo researchers who are interested in annotation and analysis. I have also updated the embryo resources as currently hosted at [eMouse Atlas] (http://www.emouseatlas.org). The code haven't changed much since the project concluded, except for some cleanup. I have moved the code from sourceforge to GitHub so that all of my projects are under my GitHub account.
This project uses the WoolzIIP protocol for retrieving embryo images. The related
woolz.js, is derived from the implementation available at
MRC Edinburgh. The WoolzIIP is
itself derived from the IIPImage project.