FlyFISH:navigation in the ADIR MFISH images database

FlyFISH allows to visualize images of the ADIR MFISH database. FlyFISH is written in python, the GUI is based on pyQt4, images are loaded and displayed with imread, qimage2ndarray. To work properly, FlyFISH requires:

• a xml description(DatabaseMFISH.xml) of the MFISH images database
• the database itself modified as previously described

The path to the DatabaseMFISH.xml file must be modified in the script:

root=et.parse('/home/simon/DatabaseMFISH.xml').getroot() 

and the path to database top directory:

workdir="/home/simon/MFISH/"

The script was tested on ubuntu 12.04, to run faster, the image size was reduced on display:

Thanks to ashren.

Navigation in an images database with a PyQt application

When recording images taken in a FISH assay, it is convenient to store them hierarchically to take into account the project, the slides, the image location on the slide, the fluorochromes used, the image itself with possible variable exposure time and possibly the variable z value  if 3D imaging is performed (only 2D will be considered).

In a previous post, a xml tree structure was proposed to store that hierarchy.
To navigate through that tree a PyQt4 widget was developed mirroring the tree:

Cascading menus are used in the GUI to navigate in the xml tree

It looks like that:

For this trial the xml tree was not complete. There are two projects, applied or vysis, but only the "applied" project has a complete slide (s1).

Version 002 of the script is here