A Transcriptome Atlas Database for Mouse Embryo
     Quick Search:    for   
Quick Help:    Sitemap      Using Context Help  
Home > Tools > Data Analysis  

FIATAS - Fast Image AnnoTAtion Software

Launch Fiatas

Click here to launch the latest FIATAS tool using Java WebStart.

Download Fiatas Sample Data Sets

Download the sample datasets. It is a zipped file named "" (approax. 52MB) containing three dataset. Unzip this file in your local computer.

Instructions for testing the Fast Image AnnoTAtion Software

The annotation tool has been developed with the idea that the editor/annotators are presented with the set of images associated with a single assay to be annotated, and an optimized anatomy ontology so the expert user can rapidly assign annotations to a given image set. Each image in the set can be independently annotated in terms of tissues/structures that show expression and the nature, strength and patterning of that expression. Comments can be added to any annotation as well as a general comment on the whole set.

The idea is that the image data to be annotated will be downloaded to the users local machine, the editor can then work without needing Internet access and the results are all saved locally. When finished, the annotation is then sent back to the tracking database and made available for the next step which could be QC/signing-off or sending onto the destination databases GenePaint and Emage.

In this test we do not have "proper" data from one of the ISH machines so we include some data sent earlier on the CDROM. These are representative images although probably at a higher resolution than necessary.

For each editor machine there is a one-off setup required to make sure that the proper version of Java and supplementary Java libraries are present. For this test we have included the annotation tool on the CDROM, in general it will be downloaded directly from HGU using the Java Webstart technology, this allows for automatic updating of the software via the Internet as well as off-line working.

1. Install Java Run Time Environment and Supporting Libraries

By default an MicroSoft Windows system does not install the proper version of Java. This must be done first for each machine and must be done by each site because there is a licence agreement from Sun MicroSystems to accept.You may want to get somebody from computing support (e.g. who has "administrator" permissions) for this or we can help by phone contact or e-mail.

  1. Download the Java Runtime Environment (JRE) from and follow the instruction to install. You need to first go to the "Downloads" page, then select JRE 5.0 Update 3 (half way down page). This brings you to a licence agreement form, choose "Accept" and press "Continue". You can now select "Windows Offline Installation.." or "Windows Online Installation, Multi-language..", either will work online probably simpler. Selecting either will result in a dialog with three options "Open", "Save", "Cancel" or "More Information", select "Open" then follow instructions, accepting the default settings. NOTE DOWN THE INSTALLATION DIRECTORY - it is probably c:\Program Files\Java\jre1.5.0_03\.
  2. Download the JavaMail package version1.3.2 from Follow the download links as above but now for JavaMail API 1.3.2. Select the (, 2.25 MB) link and open in WinZip. Drag the mail.jar file to the lib\ext\ directory within the JRE installation directory (from above).
  3. Download the JavaBean Activation Framework version 1.0.2 from, select the "Download" button (down the page), then "download" again (under "Or, feel free to download now without registration.") which you can do without registering. Again "Accept" and "Continue" then select the (, 351.36 KB) link. Open in WInZip and copy the activation,jar file to the same directory as above.

2. Copy Example Data Sets to Local Hard Disk

Copy the zip file "" to local hard disk, for example "c:/". Use WinZip to unzip it. A directory called "annotationjobs" would be created. The 3 sample data sets are within the directory "annotationjobs". Remember the path to this annotationjobs directory. In general each editor/annotator will have a personal working directory holding annotationjobs "in progress".

3. Launch the Fast Image AnnoTAtion Software (FIATAS)

This can be done in two ways:

EITHER double click on the file "fiatas.bat" on the CDROM
OR click on the link

4. Startup

To get the annotation interface going you need to set the path to the annotationjobs directory selected above. It will open without the "Annotation Jobs" dialog. For this you need to set the path to the jobs directory set above when you copied the zip file from the CDROM.

Select on the menu "Option-> Preferences" on the main window, click on the tab "Path" and set the annotation jobs path to "annotationjobs" directory set above. You can use the file browser button to locate this, navigate and select the annotationjobs directory then press "Choose". The "Annotation Jobs" windows should now show all the jobs. There are 3 sets of data in the example data set. Double click one of these jobs, the images and the annotated information will then show in the main window. You will see that one is "new", one "partial" and the other "complete". The status of job is set by the user. At the meeting in July we need to discuss the precise annotation protocol and define the status options for each assay and who has responsibility to completion and sign-off. Once the assay has been read in then you can reset the status using the "Assign" menu.

Click on the tab "E-Mail", enter your mail host to the text box. Your computer administrator would help you. Put your e-mail address to "Mail from". You can change the "Mail to" address. The DEFAULT TRACKING DATABASE E-MAIL IS "". When you choose "Assign-> Sign Off", the annotation result would send to Tracking Database automatically.

5. Annotation

Once you have selected and loaded an "annotation job" then you should see an image on the left-hand side and a tree-view on a selected set of anatomical components on the right-hand side. You can adjust the image view using the sliders (rolling thenwheel on the mouse) and zoom control to get up 3X magnification of the original image data. The view position can be adjusted by the edge sliders or by simply dragging the image. The "Backward", "Forward" and choice-box at the bottom of the image view allow selection of other images associated with this assay. Note the whole display can be re-sized and the proportion allocated to the image adjusted using the sliding vertical divider.

The tree view displays the currently selected view, in this case there are three options "simple", "organ sys" and "full. These are anatomy trees which are sub-sets of the full TS23 ontology from Emap. They are configurable and these are merely representative. An important task at the meeting in July is to define the initial annexation tree and to work out the process by which the selection is optimized and refined.

To annotate and image then click the corresponding tissue and select from the popup menus the expression strength and type (graded, homogeneous etc) the strength will be indicated as a colored text. You can also add noted to each annotation. Note in each case the annotation is to a specific tissue with a unique identifier. It does not matter which tree is used to annotate "sensory organ" under the "simple" tree is the same as "sensory organ" under the "organ sys" tree, Off course is the same as "sensory organ" under the "full" tree. You can see this by annotating in one tree and then viewing the other - it should have been set to the same co lour and have the same notes (try it). Fiatas will remember the annotation steps, this allows you "Undo and "Redo" the previous steps.

Once you think the annotation is complete, the status can be changed using the "Assign" menu. If you select "Sign off" the a dialogue will appear prompting you to enter your email address and mail server. This will appear once for the first time. When you select "OK" the report will be sent automatically to the tracking database.The next time you sign-off an annotation job the report will be sent automatically.

6. Try all the Menus and Buttons

The best way to get familiar with the FIATAS is to try all the enabled menus and buttons. You can generate a report of the annotation that will show in your web-browser. This is currently minimalist - what do we need here?

7. Feedback

Any suggestion and comments would take into implementation. At the meeting in July we need to design the next version which require a good definition of the process. At the moment the assumption is that all annotation will be by direct observation by an expert. We can add image processing tools to assist the process for example image enhancement, automatic high-lighting of potential gene-expression , perhaps even mapping to a standard view. We could also provide a window of a pre-segmented view in terms of anatomy to assist recognition of structures and so. Please think of what may be useful.