Start_NeuroGPS.wiki
Now that we have the 3D images, it is possibile to find neurons using NeuroGPS. Firstly, we have to download NeuroGPS: this is possibile from the sourceforge.net website. (download NeuroGPS, precisey following Released /NeuroGPS-Tree Software1.1.zip)
Note that NeuroGPS is available only for Windows.
Once dowloaded NeuroGPS, it is possibile to use it. To start the process of neurons' search, NeuroGPS needs three parameters:
- The voxel size of the 3D image input: this is a very important value.
- The binary treshold is used to to roughly discriminate between the foreground and background. Generally, a small trace threshold corresponds to the strong background, and a big trace threshold corresponds to the weak background.
- The minimum radius is used to screen the suspected soma positions.
It is important to find a good combination of treshold and minimum radius values to obtain satisfyng outputs by NeuroGPS. The binary treshold serves to the binarization process, the minimum radius for the probing. After the computation, an .swc output is obtained; there are annotated the neurons found by NeuroGPS.
A more detailed User Guide of NeuroGPS ( where system requirements, installation procedure and more are specified) is available for dowload here, precisely clicking on NeuroGPS-Tree User Guide.zip.
The NeuroGPS User Interface.