Implements a web app to view, annotate and organise 3D embryo models.
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lib
resources
.gitignore
LICENSE
README.md
about.html
add2DMarker.php
add2DRegion.php
addResourceToAnnotation.php
checkIntegrity.php
create2DMarker.html
create2DRegion.html
create3DMarker.html
create3DMarker.php
createLayer.html
createLayer.php
createLayerForm.php
createMarker.php
createMarkerForm.php
createModel.html
createModel.php
createOrientation.html
createOrientation.php
createOrientationForm.php
createRegion.php
createRegionForm.php
createResource.html
createResource.php
createResourceForm.php
createResourceItem.php
createResourceItemForm.php
databaseConnection.php
deleteAnnotation.php
deleteLayer.php
deleteOrientation.php
deleteResource.php
deleteResourceItem.php
dev.php
get2DMarkers.html
get2DRegions.html
get3DMarkers.html
get3DMarkers.php
getAnnotationResources.php
getLayers.php
getMarkersAndResources.php
getModels.html
getModels.php
getOrientationLayerAnnotation.php
getOrientations.php
getRegionsAndResources.php
getResource.html
getResources.php
help.html
index.html
index.php
login.php
loginForm.php
logout.php
move2dm.php
move2dr.php
ngembryo.php
onesearch.php
register.php
search.php
searchForm.php
ulinkResourceFromAnnotation.php
updateAnnotation.php
updateAnnotationForm.php
updateLayer.php
updateLayerForm.php
updateResource.php
updateResourceForm.php
updateUser.php
updateUserForm.php
utils.php

README.md

ngembryo

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.

Installation

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.

  1. Enable PHP, by uncommenting PHP5 module (LoadModule php5_module libexec/apache2/libphp5.so).

     $ sudo vi /etc/apache2/httpd.conf
    
  2. Ensure that MySQL server is accessible to PHP.

     $ sudo cd /var
     $ sudo mkdir mysql
     $ sudo ln -s /tmp/mysql.sock /var/mysql/mysql.sock
    
  3. We will use the user's Sites directory to deploy ngembryo. Create the Sites directory if it does not exists.

     $ whoami
     user
    
     $ cd ~
     $ mkdir Sites
    
  4. Download the source code:

     $ cd Sites
     $ git clone https://github/gyaikhom/ngembryo.git
     $ cd ngembryo
    
  5. Install the database, and check that it is accessible to user ngembryo.

     $ pwd
     /Users/user/Sites/ngembryo
    
     $ cd resources
     $ mysql -u root < ngembryo.sql
    
  6. 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>
    
  7. Start apache server

     $ sudo apachectl start
    
  8. Visit http://localhost:80/~user/ngembryo. Register as user, and ngembryo is ready for use.

History

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 about.html page.

Code release

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.

Acknowledgement

This project uses the WoolzIIP protocol for retrieving embryo images. The related code, especially woolz.js, is derived from the implementation available at MRC Edinburgh. The WoolzIIP is itself derived from the IIPImage project.