After your images have been imported to TrakEM2 and aligned (see here), the project needs to be organized in order to start the reconstruction.
1.Basically there a two columns: template and Project objects in the project window. You have to build up a template from where you can drop the specific templates to the project list.
![](http://stefischer.de/wp-content/uploads/2019/06/image10-1.png)
2. start by right clicking on „anything“, hit rename and give it your projects name
![](http://stefischer.de/wp-content/uploads/2019/06/image16.png)
3. next right click on your project –> add new child –> new
![](http://stefischer.de/wp-content/uploads/2019/06/image17.png)
by this we can build up a logical project tree having the diffent structures you want to segment organized.
![](http://stefischer.de/wp-content/uploads/2019/06/image18.png)
4. in the next step we connect an area_list to the structures:
![](http://stefischer.de/wp-content/uploads/2019/06/image19.png)
5. after finishing the template we can drag and drop the folders from the left to the project on the right
![](http://stefischer.de/wp-content/uploads/2019/06/image20.png)
6.now one or even several area lists can be connected with the structures
![](http://stefischer.de/wp-content/uploads/2019/06/image21.png)
![](http://stefischer.de/wp-content/uploads/2019/06/image22.png)
7.) Now we can start to reconstruct the first structures.