ImAnno

ImAnno is the Image Annotation Tool

Definition

ImAnno is a web based annotation tool.

It allows the annotation of all kind of images, texts, "concepts" through a web interface.
The annotations are stored in the relational database and can be retrieved and queried through a powerfull search engine.

First Goal of ImAnno

The first goal of ImAnno was to allow the annotation of thousands of the In Situ Hybridization images provided by GenePaint within the EurExpress project. This annotation program is a part of the Genoret project developped by WP4. See the Poster of ImAnno made by Laura Cammas for the Midterm Review Meeting 2007/03/18-21 in Paris

• ImAnno Standard Operation Procedure
• ImAnno Search Tool
• See the Rapport de Stage from Nicolas Eschbach

What is stored

One annotation is related to one or several images (or even something else). The images are referenced by local or foreign http links. These links are stored in the database and can be sorted manually. The display of the image is made through these links using the "show image" button.

An annotation consists of several annotation fields :
For each annotation field are defined

• a title
• 2 or more radio buttons with exclusive choice
• a keywords select field
• a freecomment field

The labels of the radio buttons and keywords can be specific to each field.

What about the images

In some cases the ImAnno annotation can be illustrated with images on which the annotation values are displayed through colors.

To create an ImAnno set of images :

1. create a colored image with Powerpoint or Inkscape
2. use the color ramp according to the tissue order (the fist one 0 is black)
3. save the file as ImAnnoTissue-organ-body-show-600.png -300 -150
4. remove the color ramp and save the same sizes with a yellow background
5. run Execute.php?ImAnnoCreatetissueFiles$organ

Another interesting tools is DecoreTree allowing the annotation and coloration of the phylogenic trees created by the Itol tools (http://itol.embl.fr).

Images Illustrations Photos

Especially for the Ear Raymond Romand took 11000 Microscope Images showing the gene expression.

The php programs refere to thes images through the function IllustrationsDir

 function IllustrationsDir ($cadre="", $organ="", $getWhat="")
 is mainly the coded directory ImAnno/Illustrations-$cadre-$organ

 and in /home/ripp/imanno/ImAnno we have the link (for Cadre=3 Organ=3)
 Illustrations-3-3 -> /genomics/link/ImagesRomand/Version2012/JPEG