Analysis of an image database with visualea

Automatical analysis of a set of root images can be done using an image database. The rhizoscan package provide a visualea dataflow for this task. To open it, doulbe click on arabidopsis pipeline at the bottom of the rhizoscan package:

../_images/arabidopsis_dataflow.png

This dataflow is made of two parts:

  1. The top one loads an image database. It contains 2 modules:
    • The first is to indicates the database file to load (see image database for details). By default it points to a little example database contained in the rhizoscan package. If you want toselect another file, double click on the top modules. It opens a file selection user interface where you can browse for the database file you want to load. You will need to have a valid database file in ini file format: see the page on image database for a description.
    • The second is the module that load all images from the database. It does not require any configuration.
  2. The bottom one extracts the root systems from all images. It has two main modules:
    • The pipeline module is the image arabidopsis image pipeline which analysis root images.
    • The lower module named run is the “start button”: to apply the image pipeline analysis to the whole database, right click on the run module then select run in the menu.